Contacts of the helix formed by residues 94 - 109 (chain K) in PDB entry 6NR8
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 GLY 94 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K GLN* 3.6 11.2 - - - -
93K ASP* 1.3 74.2 - - - +
95K THR* 1.3 60.1 + - - +
96K THR* 3.2 7.5 + - - +
97K SER* 2.8 34.0 + - - -
98K VAL* 2.9 21.5 + - - +
501K VAL* 5.0 5.6 - - - -
505K THR* 4.3 4.5 - - - -
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Residues in contact with THR 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K ASP* 4.0 7.8 + - - -
64K ASN* 2.9 28.1 + - - +
84K SER* 3.4 32.0 + - - +
85K ARG* 4.7 0.4 - - - +
87K GLN* 3.7 9.6 - - + -
88K ASP* 3.5 18.9 + - + +
92K GLY 3.3 20.7 + - - +
93K ASP 3.4 0.4 - - - -
94K GLY* 1.3 76.8 + - - +
96K THR* 1.3 65.2 + - - +
98K VAL* 3.8 4.2 + - - +
99K ILE* 3.5 28.2 - - - +
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Residues in contact with THR 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K ILE* 3.5 25.4 - - + +
40K CYS* 5.5 4.3 - - + +
41K LEU* 3.4 23.4 - - - +
61K ASN 4.1 19.1 - - - +
62K ASP* 4.8 11.2 - - - +
63K GLY 5.1 2.9 - - - +
64K ASN* 5.2 1.3 - - - +
94K GLY* 4.5 5.2 + - - +
95K THR* 1.3 82.9 + - - +
97K SER* 1.3 66.0 + - - +
99K ILE* 3.6 2.7 - - - +
100K ILE* 3.3 29.2 - - - +
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Residues in contact with SER 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K LEU* 3.6 19.8 - - - +
94K GLY* 2.8 19.6 + - - -
96K THR* 1.3 81.3 + - - +
98K VAL* 1.3 64.5 + - - +
99K ILE 3.4 0.2 - - - -
100K ILE* 3.3 14.2 - - - +
101K LEU* 3.3 27.0 - - - +
501K VAL* 5.3 5.4 - - - +
505K THR* 4.5 12.1 - - - -
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Residues in contact with VAL 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K MET* 5.9 0.2 - - - -
83K ILE* 4.0 26.5 - - + +
84K SER* 5.7 0.7 - - - +
87K GLN* 3.3 26.5 - - + +
94K GLY 2.9 19.1 + - - +
95K THR* 3.8 4.7 + - - +
96K THR 3.5 0.2 - - - -
97K SER* 1.3 77.7 - - - +
99K ILE* 1.3 64.0 + - + +
101K LEU* 3.2 14.0 + - - +
102K ALA* 3.4 12.8 + - + +
505K THR* 3.7 16.4 - - + -
508K THR* 3.3 35.0 - - - +
509K ALA* 4.0 10.2 - - - +
512K THR* 5.2 0.7 - - - +
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Residues in contact with ILE 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K ALA 4.6 2.6 - - - +
33K ILE* 4.0 26.1 - - + +
34K ALA* 3.8 9.1 + - - +
37K ILE* 3.8 27.1 - - + -
63K GLY* 6.3 1.8 - - - -
64K ASN* 5.6 5.2 - - - +
67K LEU* 5.3 6.1 - - + -
80K MET* 3.8 41.0 - - + +
83K ILE* 4.6 4.0 - - + -
84K SER* 3.4 25.1 - - - +
95K THR 3.5 16.6 - - - +
96K THR* 3.6 7.9 - - - +
98K VAL* 1.3 77.7 - - + +
100K ILE* 1.3 64.8 + - + +
101K LEU 3.6 0.2 + - - -
102K ALA 4.3 0.4 - - - -
103K GLY* 3.8 14.2 + - - -
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Residues in contact with ILE 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K ALA* 3.7 22.8 - - + +
37K ILE* 3.8 13.7 - - + +
38K ARG* 3.5 30.5 - - + +
41K LEU* 3.8 30.5 - - + -
96K THR 3.3 20.6 - - - +
97K SER* 3.3 19.3 - - - +
99K ILE* 1.3 77.6 - - - +
101K LEU* 1.3 66.2 + - + +
104K GLU* 3.3 23.2 + - - +
447K ILE* 3.8 31.0 - - + +
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Residues in contact with LEU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K SER* 3.3 22.2 - - - +
98K VAL 3.2 7.4 + - - +
100K ILE* 1.3 81.3 - - + +
102K ALA* 1.3 64.8 + - - +
104K GLU* 3.4 4.2 + - + +
105K MET* 3.1 32.9 + - + +
415K GLU* 3.3 27.4 - - - +
443K ALA 5.5 1.3 - - - +
444K LEU* 3.9 21.3 - - + -
447K ILE* 4.4 9.2 - - + -
505K THR* 4.2 16.2 - - - +
506K TYR* 3.7 31.6 - - + -
509K ALA* 3.7 9.9 - - + -
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Residues in contact with ALA 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K MET* 3.8 22.4 - - + -
98K VAL* 3.4 10.2 + - + +
101K LEU* 1.3 78.4 - - - +
103K GLY* 1.3 52.2 + - - +
105K MET* 3.3 15.4 + - - +
106K LEU* 2.7 34.3 + - - +
509K ALA* 3.5 22.9 - - - +
512K THR* 4.3 10.1 - - - -
513K ALA* 4.3 9.9 - - + +
516K LEU* 5.8 0.4 - - + -
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Residues in contact with GLY 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K ILE* 5.3 0.5 - - - +
30K ALA* 4.0 26.9 - - - -
31K LYS* 4.5 9.4 - - - +
34K ALA* 4.9 2.2 - - - -
80K MET* 4.3 1.8 - - - +
99K ILE 3.8 11.8 + - - -
101K LEU 3.4 0.4 - - - -
102K ALA* 1.3 76.2 - - - +
104K GLU* 1.3 59.4 + - - +
106K LEU* 3.5 10.0 - - - +
107K SER* 2.8 30.0 + - - -
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Residues in contact with GLU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K LYS* 5.4 7.6 - - - +
34K ALA* 4.9 3.6 - - + +
38K ARG* 4.1 18.4 + - - -
100K ILE 3.3 22.2 + - - +
101K LEU* 3.4 5.5 + - - +
102K ALA 3.3 0.4 - - - -
103K GLY* 1.3 74.3 - - - +
105K MET* 1.3 59.8 + - - +
107K SER* 3.9 3.9 - - - -
108K VAL* 3.0 55.2 + - - +
443K ALA* 3.3 28.9 - - + +
446K VAL* 3.5 29.7 - - + +
447K ILE* 5.0 5.7 - - + +
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Residues in contact with MET 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K LEU* 3.1 25.2 + - + +
102K ALA* 3.7 7.9 - - - +
104K GLU* 1.3 74.4 - - - +
106K LEU* 1.3 64.4 + - - +
109K ALA* 3.2 29.1 + - - +
110K GLU* 4.0 1.2 + - - +
126K TYR* 4.0 35.6 + - + +
440K VAL* 4.4 22.7 - - + +
443K ALA* 3.7 21.8 - - + -
444K LEU* 5.2 11.4 - - + -
509K ALA* 3.7 34.8 - - + +
510K VAL* 4.5 8.7 - - + +
513K ALA* 4.5 1.3 - - + -
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Residues in contact with LEU 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K ASN* 3.3 39.0 - - + +
27K ILE* 3.4 14.3 - - + +
30K ALA* 3.9 15.9 - - + -
102K ALA 2.7 20.5 + - - +
103K GLY* 3.5 5.8 - - - +
105K MET* 1.3 76.0 - - - +
107K SER* 1.3 59.4 + - - +
110K GLU* 3.3 51.1 - - + +
126K TYR* 5.0 4.7 + - - +
513K ALA* 4.6 14.4 - - + +
516K LEU* 4.2 33.7 - - + +
517K LEU* 4.8 2.2 - - + +
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Residues in contact with SER 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K ILE* 3.8 16.9 - - - +
31K LYS* 3.3 32.6 - - - +
103K GLY 2.8 16.4 + - - -
104K GLU* 3.9 6.1 - - - -
105K MET 3.2 0.2 - - - -
106K LEU* 1.3 81.1 - - - +
108K VAL* 1.3 67.1 + - - +
109K ALA 3.6 0.2 + - - -
110K GLU 4.0 1.2 + - - -
111K HIS* 3.0 25.8 + - - +
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Residues in contact with VAL 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K GLU* 3.0 39.4 + - + +
107K SER* 1.3 81.3 - - - +
109K ALA* 1.3 61.1 + - - +
111K HIS* 3.1 27.1 - - + -
112K PHE* 3.2 9.4 - - + -
439K ALA* 3.9 19.5 - - + +
442K GLN* 4.4 13.9 - - + -
443K ALA* 4.5 9.2 - - + +
446K VAL* 5.5 1.8 - - + -
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Residues in contact with ALA 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K MET* 3.2 16.0 + - - +
108K VAL* 1.3 80.5 - - - +
110K GLU* 1.3 63.9 + - - +
112K PHE* 3.2 17.8 - - - -
113K LEU* 3.3 21.9 - - + +
122K VAL* 5.4 6.7 - - + -
126K TYR* 5.5 1.1 - - - +
436K PRO 5.0 0.4 - - - +
439K ALA* 3.9 27.1 - - + -
440K VAL* 3.9 20.6 - - + -
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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
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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