Contacts of the helix formed by residues 91 - 110 (chain I) in PDB entry 6NRB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 91 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I VAL* 3.3 19.0 - - + +
35I SER 4.0 4.9 - - - +
36I LEU* 3.2 42.1 - - - +
37I GLY* 3.8 11.2 + - - +
56I ASN 4.0 2.0 - - - +
57I ASP* 4.7 1.1 - - - -
58I GLY* 3.4 24.9 - - - +
89I GLY 5.1 1.6 + - - -
90I THR* 1.3 86.7 + - - +
92I SER* 1.3 72.2 + - - +
93I VAL 3.5 0.2 - - - -
94I VAL* 3.2 17.0 + - - +
95I ILE* 4.0 5.9 + - - +
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Residues in contact with SER 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I LEU* 4.5 9.9 - - - +
89I GLY* 3.5 22.6 + - - -
91I THR* 1.3 83.5 + - - +
93I VAL* 1.3 65.4 + - - +
94I VAL 3.1 1.0 + - - -
95I ILE 3.7 6.6 + - - -
96I ILE* 4.5 1.9 + - - +
416I GLU* 6.0 1.6 - - - -
448I ILE* 3.9 22.9 - - - +
505I GLU* 5.3 2.8 + - - -
510I LYS* 4.5 14.5 + - - -
513I SER* 4.6 9.4 - - - -
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Residues in contact with VAL 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU* 3.4 38.8 - - + +
79I ALA* 3.7 6.1 - - - +
82I GLN* 4.5 2.0 - - + -
89I GLY* 3.1 22.4 + - - +
92I SER* 1.3 79.1 - - - +
94I VAL* 1.3 70.3 + - + +
95I ILE 3.2 0.3 + - - -
96I ILE* 3.5 2.4 + - - +
97I ALA* 2.9 28.1 + - + +
513I SER* 4.9 8.2 + - - -
516I PHE* 3.3 47.8 - - + +
517I ALA* 3.8 6.9 - - - +
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Residues in contact with VAL 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ILE 4.1 0.9 - - - +
29I ALA* 3.5 32.6 - - - +
32I VAL* 3.6 28.9 - - + -
62I LEU* 4.6 1.6 - - + -
75I LEU* 3.5 24.4 - - + +
79I ALA* 3.7 18.8 - - + -
90I THR 3.2 26.2 - - - +
91I THR 3.5 8.5 - - - +
92I SER 3.1 1.6 - - - -
93I VAL* 1.3 79.4 - - + +
95I ILE* 1.3 64.3 + - - +
97I ALA* 3.4 1.9 + - - +
98I ALA 3.3 15.2 + - - -
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Residues in contact with ILE 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I ALA* 4.3 1.1 - - - +
32I VAL 5.4 0.4 - - - -
33I LYS* 3.6 47.9 + - + +
36I LEU* 3.9 18.8 - - + -
91I THR 4.4 7.2 - - - +
92I SER 3.7 0.4 + - - -
93I VAL 3.3 0.8 - - - -
94I VAL* 1.3 80.1 - - + +
96I ILE* 1.3 63.6 + - - +
98I ALA* 3.5 15.8 + - - +
99I GLU* 3.8 9.0 + - - +
447I VAL* 3.6 28.5 - - + -
448I ILE* 3.6 19.5 - - + -
451I THR* 3.2 37.0 - - + +
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Residues in contact with ILE 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I SER 4.5 1.5 + - - +
93I VAL 3.5 4.0 + - - +
95I ILE* 1.3 72.2 - - - +
97I ALA* 1.3 55.0 + - - +
98I ALA 3.1 2.2 - - - -
99I GLU* 2.7 40.4 + - + +
100I LEU* 2.7 46.8 + - + +
416I GLU* 5.1 2.0 - - - +
441I PHE* 4.3 9.2 - - + -
444I SER* 3.2 36.6 - - - +
445I LEU* 4.3 15.9 - - + -
447I VAL* 3.9 7.4 - - + -
448I ILE* 3.9 21.1 - - + -
517I ALA* 4.9 7.6 - - + -
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Residues in contact with ALA 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I LEU* 3.6 24.5 - - + -
78I LEU* 4.2 1.1 - - + -
93I VAL* 2.9 32.6 + - + +
94I VAL 3.7 0.2 - - - +
95I ILE 3.3 0.2 - - - -
96I ILE* 1.3 78.6 - - - +
98I ALA* 1.3 60.2 + - - +
99I GLU 3.5 0.2 + - - -
100I LEU* 4.5 0.4 - - - +
101I LEU* 3.3 28.7 + - - +
516I PHE 4.6 1.3 - - - +
517I ALA* 4.3 8.8 + - - +
520I ALA* 3.5 22.5 - - + +
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Residues in contact with ALA 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I VAL 4.6 1.2 - - - +
25I ALA* 3.1 44.2 - - - +
26I ALA* 3.5 8.9 - - + +
29I ALA* 3.5 11.9 - - + -
33I LYS* 5.0 1.6 - - - +
75I LEU* 4.8 1.7 - - + +
94I VAL 3.3 4.2 + - - -
95I ILE 3.5 12.3 - - - +
96I ILE 3.1 0.4 - - - -
97I ALA* 1.3 80.6 - - - +
99I GLU* 1.3 61.5 + - + +
101I LEU* 3.8 5.9 - - - +
102I LYS* 3.3 22.1 + - - +
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Residues in contact with GLU 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LYS* 5.7 2.5 + - - +
95I ILE* 3.9 13.8 - - - +
96I ILE* 2.7 26.0 + - + +
98I ALA* 1.3 74.6 - - + +
100I LEU* 1.3 50.8 + - - +
102I LYS* 3.0 12.3 + - + +
103I ASN* 2.3 54.2 + - - +
443I ARG* 4.0 14.0 + - - +
444I SER* 2.7 30.7 + - - +
447I VAL* 3.5 27.6 - - - +
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Residues in contact with LEU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I ILE* 2.7 28.2 + - + +
97I ALA 3.9 1.3 + - - +
99I GLU* 1.3 68.7 - - - +
101I LEU* 1.3 56.6 + - - +
103I ASN* 3.4 19.2 - - - +
104I ALA* 2.3 40.5 + - - +
121I TYR* 3.5 27.8 - - + -
441I PHE* 3.6 35.7 - - + -
517I ALA* 3.1 39.7 - - + +
518I THR* 3.9 9.6 - - - +
521I ALA* 3.6 12.1 - - + -
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Residues in contact with LEU 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I VAL* 3.6 21.3 - - + +
25I ALA* 3.6 20.4 - - + -
71I ALA* 3.6 31.2 - - + +
74I VAL* 3.9 7.6 - - + -
75I LEU* 5.9 0.9 - - + -
97I ALA 3.3 22.4 + - - +
98I ALA 3.8 1.6 - - - +
100I LEU* 1.3 78.5 - - - +
102I LYS* 1.3 73.5 + - - +
104I ALA 4.2 0.4 - - - +
105I ASP* 3.5 28.1 + - - +
520I ALA* 3.1 35.4 - - + +
521I ALA* 3.5 14.9 - - - +
524I ILE* 4.5 7.4 - - + -
57L MET* 3.8 7.8 - - + +
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Residues in contact with LYS 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I VAL* 3.5 44.4 + - + +
23I MET* 6.2 0.6 - - - +
26I ALA* 5.3 10.1 - - + +
98I ALA 3.3 14.8 - - - +
99I GLU* 3.0 15.2 + - + +
101I LEU* 1.3 81.7 - - - +
103I ASN* 1.3 62.5 + - - +
106I GLU* 3.7 21.0 + - - +
443I ARG* 5.6 4.5 - - - +
471L LEU* 4.9 14.8 - - + +
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Residues in contact with ASN 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I GLU* 2.3 43.8 + - - +
100I LEU* 2.9 15.5 + - - +
102I LYS* 1.3 76.1 - - - +
104I ALA* 1.3 57.0 + - - +
106I GLU* 3.1 23.3 - - - +
107I LEU 4.5 0.3 + - - -
121I TYR* 2.3 27.1 + - + +
440I GLU* 2.8 54.3 + - + +
443I ARG* 2.4 29.8 + - - +
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Residues in contact with ALA 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I LEU 2.3 29.3 + - - +
101I LEU 4.2 0.2 - - - +
102I LYS 3.4 0.2 - - - -
103I ASN* 1.3 68.0 - - - +
105I ASP* 1.3 78.0 + - - +
106I GLU 2.9 4.1 + - - -
107I LEU 3.3 3.6 + - - -
108I VAL* 3.2 23.6 + - + +
117I VAL* 3.7 2.9 - - - +
121I TYR* 3.2 19.1 - - + -
521I ALA* 3.5 24.2 - - + -
522I ILE* 4.5 8.3 - - + -
525I LEU* 4.5 2.0 - - + -
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Residues in contact with ASP 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I LEU 3.5 12.6 + - - +
104I ALA* 1.3 83.3 - - - +
106I GLU* 1.3 56.6 + - - +
108I VAL* 3.8 10.1 - - - -
109I LYS* 2.8 26.2 + - - +
521I ALA 3.5 5.2 - - - +
524I ILE* 3.6 4.0 - - - +
525I LEU* 3.1 31.2 - - + +
56L GLY 4.1 0.2 - - - -
57L MET* 3.1 40.2 - - + +
469L ALA* 3.1 29.0 - - - +
470L GLY* 3.4 2.1 - - - -
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Residues in contact with GLU 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I LYS 3.7 14.8 + - - +
103I ASN* 3.1 26.9 - - - +
104I ALA 2.9 0.6 + - - -
105I ASP* 1.3 80.5 - - - +
107I LEU* 1.3 82.7 + - + +
109I LYS* 3.6 1.9 + - - +
110I GLN* 3.5 11.8 + - - +
440I GLU* 3.2 34.1 - - - +
470L GLY* 3.5 1.7 - - - -
471L LEU* 2.9 72.2 + - + +
472L ASN* 4.7 5.0 - - - +
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Residues in contact with LEU 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ALA 3.3 1.4 + - - -
106I GLU* 1.3 92.5 - - + +
108I VAL* 1.3 67.3 + - - +
109I LYS 3.1 2.2 - - - -
110I GLN* 2.9 45.8 + - - +
111I LYS* 3.6 4.5 + - - -
117I VAL* 3.4 23.8 - - + +
121I TYR* 3.9 7.6 - - - +
433I ARG* 3.3 12.9 - - + +
436I LEU* 3.4 26.7 - - + -
437I ALA* 3.2 43.3 - - + +
440I GLU* 5.0 1.1 - - + -
471L LEU 5.1 0.9 - - - +
472L ASN* 5.3 3.1 - - - +
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Residues in contact with VAL 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I ALA* 3.2 19.2 + - + +
105I ASP* 3.6 7.0 - - - +
107I LEU* 1.3 76.6 - - - +
109I LYS* 1.3 60.9 + - - +
111I LYS* 3.3 21.3 - - - +
114I PRO* 3.5 18.3 - - + +
117I VAL* 3.6 17.7 - - + +
118I ILE* 3.7 17.0 - - + -
525I LEU* 3.6 30.7 - - + -
54L PRO* 2.9 29.6 - - + +
55L LYS* 4.7 1.3 - - - +
469L ALA* 4.4 3.1 - - + -
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Residues in contact with LYS 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I ASP 2.8 8.2 + - - +
106I GLU 3.7 3.4 - - - +
108I VAL* 1.3 72.6 - - - +
110I GLN* 1.3 53.5 + - - +
111I LYS* 2.7 16.6 + - - -
55L LYS* 6.0 1.3 - - - -
466L ALA* 2.9 37.4 + - - +
467L GLU 3.1 19.2 + - - +
468L ASN 4.5 0.2 - - - -
469L ALA* 3.3 9.2 - - + +
470L GLY 3.1 51.1 - - - +
471L LEU 4.3 0.7 - - - +
473L PRO* 3.1 50.7 + - + +
476L THR* 3.2 10.4 + - - -
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Residues in contact with GLN 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456G ASP* 5.0 1.0 + - - -
458G THR* 5.8 0.6 - - - -
106I GLU 3.5 10.8 - - - +
107I LEU* 2.9 39.9 + - - +
109I LYS* 1.3 75.9 - - - +
111I LYS* 1.3 63.4 + - - +
112I ILE 3.4 1.4 + - - -
433I ARG* 3.2 47.4 + - + +
436I LEU* 4.6 1.6 - - - +
471L LEU 3.6 2.2 - - - +
472L ASN* 2.8 48.6 + - - +
473L PRO* 4.1 4.3 - - + +
475L SER* 4.0 16.9 + - - +
476L THR* 2.8 16.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il