Contacts of the helix formed by residues 67 - 84 (chain P) in PDB entry 5GAG
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 ASN 67 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B A 3.2 20.9 - - - +
51B G 3.5 30.9 + - - +
62P LEU* 5.4 0.2 - - - +
63P LYS* 5.0 4.6 - - - +
64P TYR* 3.4 30.6 + - - +
65P THR 3.7 1.6 - - - -
66P GLY* 1.3 79.7 - - - +
68P LYS* 1.3 64.1 + - - +
69P ASP* 3.3 20.0 + - - +
70P ALA* 3.0 34.0 + - - +
71P ALA 3.2 4.5 + - - -
102P ARG* 3.6 11.5 - - - -
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Residues in contact with LYS 68 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B C 3.5 20.8 + - - -
49B C 3.1 45.3 + - - -
50B A 3.1 10.4 + - - +
67P ASN* 1.3 74.6 - - - +
69P ASP* 1.3 64.9 + - - +
71P ALA* 3.2 5.6 + - - +
72P ALA* 2.9 27.2 + - - +
101P GLY* 4.1 13.7 - - - +
102P ARG* 4.0 26.9 - - + +
105P ALA* 4.0 12.3 - - + +
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Residues in contact with ASP 69 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62P LEU* 4.3 8.3 - - + +
67P ASN* 3.3 18.6 + - - +
68P LYS* 1.3 77.0 - - - +
70P ALA* 1.3 59.9 + - - +
72P ALA* 3.3 8.6 + - - +
73P ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P ILE* 4.6 5.2 - - + -
53P THR* 4.1 4.7 - - + -
62P LEU* 4.0 25.5 - - + +
64P TYR 4.0 0.4 - - - +
65P THR 3.7 28.5 - - - +
66P GLY 4.6 0.2 - - - -
67P ASN* 3.0 24.2 + - - +
69P ASP* 1.3 73.4 - - - +
71P ALA* 1.3 58.4 - - - +
73P ALA* 3.1 3.5 + - - +
74P VAL* 2.9 35.3 + - - +
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Residues in contact with ALA 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P ILE* 4.1 19.6 - - + +
67P ASN 3.2 7.2 + - - +
68P LYS 3.2 10.3 + - - +
70P ALA* 1.3 76.9 - - - +
72P ALA* 1.3 57.2 + - - +
75P GLY 2.9 23.2 + - - -
102P ARG* 3.2 37.9 - - + +
105P ALA* 3.8 3.1 - - + -
106P LEU* 3.3 22.7 - - + +
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Residues in contact with ALA 72 (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 LYS 2.9 12.9 + - - +
69P ASP* 3.4 13.2 - - - +
70P ALA 3.1 0.2 - - - -
71P ALA* 1.3 73.8 - - - +
73P ALA* 1.3 60.3 + - - +
75P GLY 3.3 0.3 + - - -
76P LYS* 2.9 31.0 + - - +
105P ALA* 4.5 7.1 - - + +
109P ALA* 3.3 17.4 - - + +
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Residues in contact with ALA 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58P ILE* 3.9 20.6 - - + +
61P GLN* 6.1 1.8 - - + -
62P LEU* 4.0 14.8 - - + -
69P ASP 2.9 16.5 + - - +
70P ALA 3.1 4.2 + - - +
72P ALA* 1.3 76.5 - - - +
74P VAL* 1.3 57.6 + - - +
76P LYS* 3.6 9.0 - - - +
77P ALA* 2.9 28.0 + - - +
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Residues in contact with VAL 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P ILE* 4.4 9.4 - - + -
37P ALA* 4.7 4.0 - - + +
51P ALA* 4.1 19.3 - - + +
52P SER* 3.7 33.4 - - - +
53P THR* 4.0 13.5 - - + +
58P ILE* 4.1 12.8 - - + -
70P ALA 2.9 16.6 + - - +
71P ALA 4.2 0.9 - - - +
73P ALA* 1.3 74.4 - - - +
75P GLY* 1.3 69.2 + - - +
77P ALA* 3.0 6.2 + - - +
78P VAL* 2.9 26.6 + - + +
106P LEU* 3.6 20.9 - - + -
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Residues in contact with GLY 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P ALA 2.9 19.6 + - - -
72P ALA 3.7 0.4 - - - -
74P VAL* 1.3 77.9 - - - +
76P LYS* 1.3 61.1 + - - +
78P VAL* 3.1 8.5 - - - +
79P ALA* 3.0 24.1 + - - +
106P LEU* 3.7 27.6 - - - -
109P ALA* 3.9 4.7 - - - -
110P ALA* 3.9 6.0 - - - -
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Residues in contact with LYS 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P ALA 2.9 18.0 + - - +
73P ALA* 3.6 8.5 - - - +
75P GLY* 1.3 74.4 - - - +
77P ALA* 1.3 55.9 + - - +
79P ALA* 3.4 1.7 + - - +
80P GLU* 2.9 57.3 + - - +
109P ALA* 3.5 16.0 - - + +
113P ALA* 4.2 12.1 - - + +
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Residues in contact with ALA 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P ALA* 4.2 4.0 - - + -
58P ILE* 3.6 29.6 - - + -
73P ALA 2.9 19.4 + - - +
74P VAL 3.0 5.4 + - - +
76P LYS* 1.3 72.6 - - - +
78P VAL* 1.3 66.2 + - - +
80P GLU* 3.2 14.6 + - - +
81P ARG* 2.9 36.9 + - - +
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Residues in contact with VAL 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P LEU* 4.9 13.7 - - + -
37P ALA* 3.9 28.7 - - + +
38P GLN* 5.0 1.1 - - - +
39P VAL* 5.2 3.8 - - + -
49P VAL* 4.5 4.7 - - + +
50P ALA* 3.8 9.2 - - - +
51P ALA* 3.4 34.3 - - + +
74P VAL* 2.9 24.3 + - + +
75P GLY* 3.1 18.8 - - - +
77P ALA* 1.3 72.8 - - - +
79P ALA* 1.3 57.5 + - - +
81P ARG* 3.8 3.9 - - - +
82P ALA* 2.9 34.2 + - - +
106P LEU* 5.1 2.9 - - + -
110P ALA* 5.1 6.3 - - + -
115P LEU* 5.7 1.1 - - + -
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Residues in contact with ALA 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P GLY 3.0 16.0 + - - +
76P LYS 3.7 0.2 - - - +
78P VAL* 1.3 77.1 - - - +
80P GLU* 1.3 58.0 + - - +
82P ALA* 3.8 1.2 - - - +
83P LEU* 2.9 36.5 + - - +
110P ALA* 3.6 23.3 - - + +
113P ALA* 3.5 28.7 - - + -
115P LEU* 4.1 18.3 - - + +
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Residues in contact with GLU 80 (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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76P LYS* 2.9 55.3 + - + +
77P ALA* 3.2 12.6 + - - +
79P ALA* 1.3 75.3 - - - +
81P ARG* 1.3 67.0 + - + +
83P LEU* 3.0 11.6 + - - +
84P GLU* 3.0 37.5 + - - +
113P ALA* 4.9 6.7 - - + +
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Residues in contact with ARG 81 (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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49P VAL* 3.4 25.3 - - + +
50P ALA 2.5 32.4 + - - -
51P ALA* 3.3 14.9 - - - +
55P GLU* 3.1 29.5 + - - -
57P ALA* 5.4 4.2 - - - +
58P ILE* 5.2 2.6 - - - +
77P ALA* 2.9 31.7 + - - +
78P VAL* 4.1 4.3 - - - +
80P GLU* 1.3 75.6 - - + +
82P ALA* 1.3 59.4 + - - +
84P GLU* 3.6 29.1 - - - +
85P LYS* 3.8 6.4 - - - +
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Residues in contact with ALA 82 (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 VAL* 4.4 9.4 - - + -
49P VAL* 3.7 21.1 - - + +
78P VAL 2.9 18.8 + - - +
79P ALA* 3.8 5.4 - - - +
81P ARG* 1.3 76.0 - - - +
83P LEU* 1.3 65.7 + - - +
84P GLU 3.0 1.6 - - - -
85P LYS* 3.0 10.6 + - - -
87P ILE* 3.2 38.9 + - + +
115P LEU* 4.7 8.3 - - + -
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Residues in contact with LEU 83 (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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79P ALA 2.9 23.9 + - - +
80P GLU* 3.0 7.2 + - + +
82P ALA* 1.3 77.1 - - - +
84P GLU* 1.3 61.7 + - + +
86P GLY* 3.2 12.8 + - - -
87P ILE 3.5 17.7 - - - +
88P LYS* 4.4 14.4 - - + -
113P ALA 3.2 27.4 - - - +
114P GLY* 3.9 22.4 - - - +
115P LEU* 4.0 9.0 - - + +
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Residues in contact with GLU 84 (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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80P GLU* 3.0 30.4 + - - +
81P ARG* 3.6 23.5 + - - +
83P LEU* 1.3 78.5 - - + +
85P LYS* 1.3 60.9 + - + +
86P GLY 3.4 0.4 + - - -
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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