Contacts of the helix formed by residues 85 - 103 (chain A) in PDB entry 5E2Q
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LEU* 4.2 1.8 - - - -
83A GLY 4.7 4.3 - - - +
84A LEU* 1.3 76.8 - - - +
86A GLU* 1.3 58.2 + - - +
87A GLU* 3.6 10.1 + - - +
88A GLU* 3.1 38.8 + - - +
89A TYR* 2.9 27.2 + - - +
122A LYS* 5.1 2.5 - - - +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.1 42.2 + - - -
80A LEU* 3.7 26.2 - - + +
85A THR* 1.3 74.5 - - - +
87A GLU* 1.3 57.5 + - - +
89A TYR* 3.8 4.7 - - - +
90A GLN* 2.9 44.8 + - + +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 3.0 35.9 + - - +
85A THR* 3.1 8.9 + - - +
86A GLU* 1.3 78.0 - - - +
88A GLU* 1.3 62.3 + - + +
90A GLN* 3.3 2.3 + - - -
91A ALA* 3.0 15.6 + - - +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.6 11.1 - - + -
85A THR* 3.1 39.9 + - - +
87A GLU* 1.3 79.1 - - + +
89A TYR* 1.3 62.4 + - - +
91A ALA* 3.3 15.4 + - - +
92A PHE* 3.3 9.0 + - - +
117A ASN 4.9 2.2 - - - +
118A LEU* 3.6 29.0 - - + +
119A PRO* 3.5 20.6 - - + +
122A LYS* 3.1 37.0 + - - +
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PRO* 2.4 36.5 + - - +
75A LEU* 3.5 20.6 - - + +
76A ARG* 3.1 43.7 + - + -
79A ALA* 3.6 28.5 - - + -
80A LEU* 4.0 11.4 - - + -
84A LEU* 4.3 12.0 - - + +
85A THR 2.9 16.8 + - - +
86A GLU* 3.8 6.1 - - - +
88A GLU* 1.3 73.6 - - - +
90A GLN* 1.3 66.3 + - - +
92A PHE* 3.0 16.2 + + - +
93A LEU* 3.0 52.6 + - + +
126A VAL* 5.8 1.1 - - + -
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 3.6 20.1 - - + +
76A ARG* 3.7 14.1 - - - +
86A GLU* 2.9 43.9 + - + +
87A GLU* 3.5 7.2 - - - +
89A TYR* 1.3 76.9 - - - +
91A ALA* 1.3 57.4 + - - +
93A LEU* 3.2 18.0 + - - +
94A VAL* 2.9 41.5 + - - +
693A ALA* 5.1 4.2 - - - +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU 5.6 2.1 - - - +
10A ASN* 3.4 20.1 + - - +
87A GLU 3.0 11.6 + - - +
88A GLU* 3.4 10.5 - - - +
89A TYR 3.2 0.2 - - - -
90A GLN* 1.3 76.7 - - - +
92A PHE* 1.3 58.5 + - - +
94A VAL* 3.6 3.9 + - - +
95A TYR* 3.1 26.5 + - - +
117A ASN* 3.3 43.8 + - + +
118A LEU* 4.3 2.5 - - + -
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.8 30.7 - - + -
66A LEU* 4.0 16.6 - - + -
67A PHE* 3.7 26.5 - + - -
75A LEU* 3.9 14.1 - - + -
84A LEU* 5.6 1.3 - - + -
88A GLU 3.3 7.6 + - - +
89A TYR* 3.0 28.5 + + + +
91A ALA* 1.3 78.1 - - - +
93A LEU* 1.3 59.9 + - + +
95A TYR* 3.6 13.6 - + - +
96A ALA* 3.0 27.5 + - - +
116A PRO* 5.3 0.4 - - + -
118A LEU* 4.1 14.5 - - + +
123A LEU* 3.5 42.6 - - + -
126A VAL* 5.7 3.4 - - + -
127A ILE* 5.3 1.8 - - + -
151A MET* 5.8 1.6 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 4.1 14.6 - - + -
72A PRO* 4.2 7.9 - - + -
76A ARG* 4.2 5.2 - - - +
89A TYR* 3.0 59.4 + - + +
90A GLN* 3.2 30.3 + - - +
92A PHE* 1.3 78.3 - - + +
94A VAL* 1.3 56.7 + - - +
96A ALA* 3.5 0.6 + - - -
97A ALA* 3.0 28.4 + - - +
693A ALA* 3.7 12.9 - - + +
694A ALA* 4.7 16.2 - - + +
697A ILE* 3.6 26.5 - - + +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.6 28.6 - - + +
9A PRO 3.5 17.0 - - - +
10A ASN* 3.8 29.2 - - - +
12A ILE* 3.7 16.4 - - + -
90A GLN* 2.9 26.2 + - - +
91A ALA* 3.8 6.1 - - - +
93A LEU* 1.3 75.2 - - - +
95A TYR* 1.3 59.5 + - - +
97A ALA* 3.7 2.5 - - - +
98A GLY* 2.9 26.3 + - - -
671A LEU* 4.5 2.4 - - + +
693A ALA* 4.2 16.2 - - + -
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.6 7.4 - - - -
59A ILE* 3.3 34.7 - - + +
63A LEU* 4.9 4.5 - - + -
91A ALA 3.1 18.4 + - - +
92A PHE* 3.3 17.5 + + - +
94A VAL* 1.3 76.6 - - - +
96A ALA* 1.3 61.1 + - - +
98A GLY* 3.0 2.9 + - - -
99A VAL* 2.9 42.9 + - + +
105A ASN* 3.9 8.6 - - + +
114A PHE* 3.3 42.7 - + - -
115A VAL 3.6 2.5 - - - +
116A PRO* 3.5 48.2 - - + -
151A MET* 3.4 19.2 + - + +
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.7 28.2 - - + +
67A PHE* 3.9 25.6 - - + -
92A PHE* 3.0 18.8 + - + +
93A LEU 3.8 4.0 - - - +
95A TYR* 1.3 76.8 - - - +
97A ALA* 1.3 58.2 + - - +
99A VAL* 3.2 3.6 + - - +
100A TYR* 3.0 36.7 + - + -
697A ILE* 3.9 7.0 - - + -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU 3.0 18.5 + - - +
94A VAL 3.7 4.3 - - - +
96A ALA* 1.3 76.3 - - - +
98A GLY* 1.3 58.1 + - - +
100A TYR* 3.5 1.0 + - - -
101A SER* 3.0 31.1 + - - -
671A LEU* 4.1 13.9 - - + -
693A ALA* 3.9 29.4 - - + +
696A LEU* 3.5 21.9 - - + +
697A ILE* 4.2 3.7 - - - +
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.8 18.8 - - - -
94A VAL 2.9 14.2 + - - -
95A TYR 3.0 4.9 + - - -
97A ALA* 1.3 74.9 - - - +
99A VAL* 1.3 64.2 + - - +
101A SER* 3.4 5.8 + - - -
102A ASN* 3.0 33.6 + - - +
114A PHE* 3.5 7.4 - - - -
671A LEU* 4.2 5.4 - - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.8 9.4 - - + -
56A ALA* 5.3 0.9 - - - +
59A ILE* 4.2 14.6 - - + -
60A TYR* 4.8 6.3 - - + +
63A LEU* 4.0 15.9 - - + -
95A TYR* 2.9 50.3 + - + +
96A ALA 3.6 6.7 - - - +
98A GLY* 1.3 75.2 - - - +
100A TYR* 1.3 59.3 + - + +
103A MET* 2.7 30.7 + - - +
104A GLY* 3.1 31.3 + - - +
105A ASN* 4.5 3.8 - - + -
114A PHE* 4.0 7.9 - - + -
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 3.5 40.4 - + - -
63A LEU* 3.5 23.3 + - + +
64A SER* 3.5 28.1 + - - -
67A PHE* 4.1 6.7 - + - +
96A ALA* 3.0 20.0 + - + +
97A ALA 3.7 0.2 - - - +
98A GLY 3.3 0.2 - - - -
99A VAL* 1.3 80.4 - - + +
101A SER* 1.3 61.6 + - - +
102A ASN 3.4 0.2 + - - -
103A MET* 3.3 24.9 + - - +
383A GLY 4.9 0.5 - - - +
696A LEU* 3.7 7.6 - - + -
697A ILE* 4.0 36.8 - - + -
700A PHE* 3.4 53.5 - + + -
701A SER* 5.4 1.8 + - - -
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA 3.0 18.1 + - - -
98A GLY 3.4 5.0 + - - -
100A TYR* 1.3 77.2 - - - +
102A ASN* 1.3 63.5 + - - +
383A GLY 4.0 4.2 - - - +
384A SER 2.9 17.3 - - - +
385A GLY* 4.5 2.6 - - - -
671A LEU* 3.5 24.4 - - - +
672A ILE 4.8 9.0 - - - -
696A LEU* 4.1 19.5 - - - -
700A PHE* 5.0 2.7 - - - -
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Residues in contact with ASN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 5.6 2.2 - - - +
48A VAL* 4.2 0.5 - - - +
98A GLY* 3.0 29.1 + - - +
101A SER* 1.3 86.2 + - - +
103A MET* 1.3 71.7 + - - +
104A GLY* 3.4 7.7 + - - +
106A TYR 3.7 16.3 - - - +
107A LYS* 3.6 9.5 - - - +
108A SER* 2.9 38.1 + - - +
114A PHE* 4.2 9.5 - - - -
319A ARG* 4.3 4.3 + - - -
384A SER* 3.2 23.9 - - - +
671A LEU* 4.8 6.5 - - - +
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Residues in contact with MET 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 3.3 29.4 - - - +
46A LEU* 4.0 10.3 - - + -
48A VAL* 3.6 16.3 - - + -
49A LEU* 3.5 32.7 + - + -
52A THR* 3.3 15.2 + - - -
60A TYR* 4.1 25.4 - - + -
99A VAL 2.7 13.0 + - - +
100A TYR* 3.3 26.1 + - - +
102A ASN* 1.3 80.0 - - - +
104A GLY* 1.3 55.4 + - - +
383A GLY* 3.3 21.3 - - - +
700A PHE* 3.9 21.3 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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