Contacts of the helix formed by residues 100 - 114 (chain P) 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 100 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P TYR* 3.9 6.5 + - - -
93P GLN* 5.1 3.6 - - - -
99P ASP* 1.3 88.5 + - - +
101P THR* 1.3 59.5 + - - +
102P ASN 3.2 0.4 - - - -
103P PHE* 3.1 24.7 + - - +
104P VAL* 2.9 30.0 + - - +
507P ALA* 4.5 7.1 - - - +
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Residues in contact with THR 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P ASP* 3.2 22.3 + - - -
69P ALA* 3.3 11.8 + - - +
70P ALA* 3.9 3.5 + - + -
90P SER* 3.3 39.7 + - - +
93P GLN* 3.8 11.7 - - + -
94P GLU* 3.4 11.9 + - + +
98P GLY 3.4 17.2 + - - +
99P ASP 3.4 0.6 - - - -
100P GLY* 1.3 75.1 - - - +
102P ASN* 1.3 65.0 + - - +
104P VAL* 3.2 18.4 + - - +
105P LEU* 3.3 19.2 + - - +
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Residues in contact with ASN 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P THR 4.4 7.3 + - - -
43P THR* 3.1 46.4 + - - +
47P TYR* 3.4 20.7 - - + +
67P ASN 3.5 10.5 + - - -
68P ASP* 3.4 7.0 - - - +
69P ALA* 3.1 29.3 - - - +
99P ASP* 3.1 10.6 - - - +
101P THR* 1.3 76.0 + - - +
103P PHE* 1.3 61.4 + - - +
105P LEU* 3.3 10.3 + - - -
106P VAL* 3.6 2.8 + - - +
171P LYS* 2.5 29.9 + - - -
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Residues in contact with PHE 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P TYR* 4.3 12.4 - + + +
100P GLY* 3.1 21.1 + - - +
102P ASN* 1.3 78.2 - - - +
104P VAL* 1.3 62.0 + - - +
106P VAL* 4.0 5.8 + - - +
107P PHE* 3.3 35.4 + + + +
412P GLY* 6.5 0.7 - - - -
416P GLU* 3.5 28.3 - - + -
448P ILE* 3.6 38.6 - - + -
504P LYS* 4.1 19.7 - - + -
507P ALA* 3.5 41.3 - - + -
508P ILE* 4.0 17.0 - - + -
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Residues in contact with VAL 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86P ILE* 3.7 24.9 - - + +
89P ALA* 4.8 7.2 - - + -
90P SER* 3.8 11.7 - - - +
93P GLN* 3.9 25.6 - - + -
100P GLY 2.9 18.6 + - - +
101P THR* 3.4 11.2 - - - +
102P ASN 3.2 0.4 - - - -
103P PHE* 1.3 79.2 - - - +
105P LEU* 1.3 56.0 + - - +
107P PHE* 4.0 0.7 - - - +
108P ALA* 3.0 29.6 + - - +
507P ALA* 3.8 20.6 - - - +
511P ALA* 4.0 22.3 - - + +
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Residues in contact with LEU 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P LEU* 3.2 34.7 - - + +
42P THR* 4.2 21.5 - - + -
43P THR* 3.9 14.4 - - + -
69P ALA* 3.7 23.3 - - + -
73P LEU* 3.8 27.4 - - + -
86P ILE* 4.0 20.9 - - + +
87P VAL* 6.1 0.2 - - + -
90P SER* 4.1 7.0 - - - +
101P THR 3.3 13.0 - - - +
102P ASN* 3.3 5.5 + - - +
104P VAL* 1.3 76.0 - - - +
106P VAL* 1.3 53.5 + - - +
109P GLY* 2.5 36.0 + - - -
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Residues in contact with VAL 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P LEU* 5.2 2.2 - - - -
43P THR* 3.7 19.5 - - + +
44P ARG* 3.6 38.1 - - + +
47P TYR* 6.3 0.2 - - + -
102P ASN 3.6 13.6 + - - +
103P PHE* 4.1 3.1 - - - +
105P LEU* 1.3 78.9 - - - +
107P PHE* 1.3 60.6 + - - +
109P GLY* 4.2 2.0 - - - +
110P ALA* 2.9 27.4 + - - +
447P ALA* 3.7 24.7 - - + +
448P ILE* 3.7 24.7 - - + -
451P ALA* 4.5 8.7 - - + -
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Residues in contact with PHE 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P PHE* 3.3 35.4 + + + +
104P VAL 4.0 0.9 - - - +
105P LEU 3.2 0.6 - - - -
106P VAL* 1.3 80.3 - - - +
108P ALA* 1.3 61.6 + - - +
110P ALA* 4.0 1.7 - - - +
111P LEU* 3.1 33.6 + - + +
416P GLU* 4.8 2.0 - - - -
441P PHE* 4.6 7.9 - + - -
444P ALA* 3.2 35.8 - - + +
445P PHE* 3.6 37.0 - + - -
447P ALA* 4.9 1.1 - - - -
448P ILE* 4.8 5.6 - - + -
507P ALA 5.1 2.2 - - - -
508P ILE* 4.6 13.7 - - + -
511P ALA* 3.6 22.7 - - + -
512P THR* 3.7 31.0 - - + -
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Residues in contact with ALA 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P LEU* 4.8 0.4 - - - -
86P ILE* 3.9 28.0 - - + -
104P VAL 3.0 18.4 + - - +
105P LEU 4.0 0.9 - - - +
107P PHE* 1.3 78.9 - - - +
109P GLY* 1.3 63.1 + - - +
111P LEU* 4.0 5.3 - - - +
112P LEU* 3.1 32.5 + - - +
511P ALA* 4.0 22.0 - - + +
515P ALA* 4.4 7.9 - - + -
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Residues in contact with GLY 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P CYS* 3.3 34.8 - - - -
39P LEU* 4.1 9.6 - - - +
44P ARG* 4.6 8.3 - - - -
105P LEU 2.5 23.1 + - - -
106P VAL* 3.8 2.7 - - - -
108P ALA* 1.3 73.7 - - - +
110P ALA* 1.3 59.1 + - - +
113P GLU* 3.3 17.0 + - - +
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Residues in contact with ALA 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ARG* 4.7 4.6 - - - +
106P VAL 2.9 19.2 + - - +
107P PHE 4.0 3.4 - - - +
109P GLY* 1.3 76.1 - - - +
111P LEU* 1.3 65.2 + - - +
113P GLU* 3.0 18.9 + - - +
114P LEU* 3.1 21.5 + - + +
444P ALA* 4.3 8.1 - - - -
447P ALA* 3.7 21.1 - - + -
450P ARG* 4.0 13.2 - - - +
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Residues in contact with LEU 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P PHE* 3.1 27.6 + - + +
108P ALA* 3.4 4.7 + - - +
110P ALA* 1.3 77.4 - - - +
112P LEU* 1.3 61.7 + - + +
114P LEU* 3.6 8.3 + - + +
115P ALA* 3.9 2.6 + - - +
132P TYR* 3.5 66.7 + - + +
440P LYS 4.2 3.4 - - - +
441P PHE* 4.1 25.4 - - + -
444P ALA* 3.7 21.1 - - + +
512P THR* 4.7 12.8 - - + -
515P ALA* 4.4 19.7 - - + -
516P VAL* 5.6 0.4 - - + -
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Residues in contact with LEU 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ASN* 4.5 20.4 - - + +
33P ILE* 5.1 0.4 - - - -
35P ALA* 6.4 0.4 - - + -
36P CYS* 3.7 24.9 - - - -
86P ILE* 4.4 13.7 - - + -
108P ALA 3.1 21.5 + - - +
111P LEU* 1.3 79.0 - - - +
113P GLU* 1.3 58.2 + - - +
114P LEU 3.4 0.7 + - - -
115P ALA* 3.4 11.0 + - - +
116P GLU* 2.8 24.3 - - - +
132P TYR* 6.6 0.4 - - + -
515P ALA* 3.5 33.9 - - + +
518P VAL* 3.8 23.1 - - + -
519P LEU* 4.2 22.2 - - + +
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Residues in contact with GLU 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P ILE* 3.9 16.5 - - + +
36P CYS* 3.2 26.2 - - + +
37P LYS* 3.0 28.7 + - - +
44P ARG* 4.4 13.7 + - - -
109P GLY 3.3 18.6 + - - +
110P ALA* 3.0 8.7 + - - +
112P LEU* 1.3 76.7 - - - +
114P LEU* 1.3 60.7 + - + +
115P ALA 3.2 0.2 - - - -
116P GLU* 3.0 13.4 - - - +
117P GLU* 2.9 22.2 - - - +
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Residues in contact with LEU 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P ALA* 3.1 20.6 + - + +
111P LEU* 4.0 7.2 - - + +
112P LEU 3.2 0.6 - - - -
113P GLU* 1.3 76.4 - - + +
115P ALA* 1.3 57.6 + - - +
117P GLU* 2.9 16.7 - - - +
132P TYR* 4.6 1.3 - - - +
440P LYS* 2.6 79.7 + - + +
443P GLU* 3.7 22.4 - - + +
444P ALA* 3.7 14.8 - - + +
450P ARG* 5.3 3.8 - - - +
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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