Contacts of the helix formed by residues 79 - 96 (chain A) in PDB entry 3EGC
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ASP* 3.0 29.5 + - - +
77A ILE 3.3 3.7 - - - +
78A GLU* 1.3 75.8 - - - +
80A VAL* 1.3 64.8 + - - +
81A PHE* 2.9 18.5 + - - +
82A PHE* 3.1 28.0 + - + -
83A ALA 3.2 9.7 + - - -
253A SER* 5.8 2.8 + - - -
254A HIS* 2.8 31.0 + - - -
255A ARG* 3.7 26.8 - - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU 3.6 2.0 + - - -
79A ASN* 1.3 73.1 + - - +
81A PHE* 1.3 68.4 + - - +
83A ALA* 3.8 6.0 - - + +
84A GLU* 3.0 43.0 + - - +
254A HIS* 4.3 12.5 + - + +
255A ARG* 4.6 0.8 - - - +
283A LEU* 4.3 30.3 - - + -
78B GLU 3.6 20.6 - - - +
80B VAL* 3.3 30.5 - - + +
255B ARG* 5.4 4.3 - - - +
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 2.9 18.7 + - - +
80A VAL* 1.3 82.3 - - - +
82A PHE* 1.3 89.6 + + + +
84A GLU* 3.4 4.3 + - - +
85A VAL* 3.1 45.4 + - + +
153A ASN* 3.8 32.1 - - + -
254A HIS* 4.4 5.1 + - + +
281A ASP* 3.9 10.5 - - - +
298A GLN* 3.3 39.3 - - + -
300A THR* 3.6 27.6 - - + +
303A ILE* 4.4 11.2 - - + -
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Residues in contact with PHE 82 (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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74A VAL* 3.6 21.7 - - + +
75A SER* 3.2 23.6 - - - -
76A ASP* 3.3 37.5 - - + +
77A ILE* 4.0 3.2 - - - +
79A ASN* 3.1 21.4 + - + -
81A PHE* 1.3 98.8 - + - +
83A ALA* 1.3 60.3 + - - +
85A VAL* 3.7 9.3 - - + +
86A ALA* 2.9 29.6 + - - +
107A GLU* 4.7 4.3 - - - -
130A ALA* 3.7 23.8 - - + -
152A VAL* 5.4 1.3 - - + -
153A ASN* 3.7 22.0 - - + -
154A ARG* 4.7 6.3 - - - -
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Residues in contact with ALA 83 (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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77A ILE* 3.7 28.7 + - + +
79A ASN 3.2 7.4 + - - +
80A VAL* 3.8 12.3 - - + +
81A PHE 3.4 0.2 - - - -
82A PHE* 1.3 76.0 - - - +
84A GLU* 1.3 58.1 + - - +
86A ALA* 3.5 1.1 + - - +
87A SER* 3.0 26.3 + - - -
77B ILE* 3.2 37.1 - - + +
78B GLU* 4.2 6.5 - - - +
83B ALA* 4.0 6.7 - - + -
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Residues in contact with GLU 84 (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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80A VAL* 3.0 36.8 + - + +
81A PHE* 3.7 0.6 - - - +
83A ALA* 1.3 75.3 - - - +
85A VAL* 1.3 63.4 + - - +
87A SER* 3.4 2.8 - - - -
88A GLY 3.2 15.6 + - - -
282A ASN 5.7 1.2 - - - +
300A THR* 2.4 47.9 + - - +
301A ARG* 3.5 34.6 + - + +
78B GLU* 3.9 32.3 - - + +
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Residues in contact with VAL 85 (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 LEU* 5.5 4.7 - - + -
74A VAL* 5.7 3.8 - - + -
81A PHE* 3.1 46.6 + - + +
82A PHE* 3.7 10.5 - - + +
83A ALA 3.4 0.2 - - - -
84A GLU* 1.3 72.6 - - - +
86A ALA* 1.3 61.8 + - - +
88A GLY 3.2 1.6 + - - -
89A VAL* 2.9 34.7 + - + +
128A ILE* 5.7 0.2 - - + -
152A VAL* 4.3 23.1 - - + -
300A THR* 3.5 22.4 - - - +
303A ILE* 4.3 11.0 - - + -
304A GLY* 3.3 18.2 - - - +
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Residues in contact with ALA 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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72A LEU* 3.7 29.6 - - + +
74A VAL* 5.2 0.9 - - + +
77A ILE* 4.1 16.8 - - + -
82A PHE 2.9 18.8 + - - +
83A ALA* 3.6 5.4 - - - +
85A VAL* 1.3 76.4 - - - +
87A SER* 1.3 53.4 + - - +
89A VAL* 3.3 4.1 + - - +
90A GLU* 2.8 36.8 + - - +
77B ILE* 5.0 3.8 - - + -
102B LEU* 4.6 12.9 - - + +
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Residues in contact with SER 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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83A ALA 3.0 15.4 + - - -
84A GLU 3.4 8.7 - - - -
86A ALA* 1.3 75.0 - - - +
88A GLY* 1.3 62.1 + - - +
90A GLU* 3.3 6.1 + - - +
91A SER* 3.0 25.9 + - - -
301A ARG* 4.4 1.7 - - - +
77B ILE* 3.8 13.6 - - - +
78B GLU* 2.7 34.6 + - - -
104B ASN* 3.4 17.4 + - - +
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Residues in contact with GLY 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 GLU 3.2 9.8 + - - -
85A VAL 3.2 2.4 + - - -
87A SER* 1.3 78.1 + - - +
89A VAL* 1.3 62.2 + - - +
91A SER* 3.6 5.3 + - - -
92A GLU* 3.1 25.8 + - - +
301A ARG* 3.4 28.9 - - - +
305A GLN* 3.5 14.5 - - - +
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Residues in contact with VAL 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 LEU* 4.4 21.1 - - + -
85A VAL* 2.9 27.1 + - + +
86A ALA* 3.3 10.7 + - - +
88A GLY* 1.3 76.2 - - - +
90A GLU* 1.3 58.9 + - - +
92A GLU 3.4 0.9 + - - -
93A ALA* 2.9 28.1 + - - +
100A VAL* 4.4 8.3 - - + -
128A ILE* 3.8 16.6 - - + -
304A GLY* 3.4 25.2 - - - +
308A MET* 2.8 37.0 - - + +
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Residues in contact with GLU 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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86A ALA 2.8 20.6 + - - +
87A SER* 3.8 5.5 - - - +
89A VAL* 1.3 75.9 - - - +
91A SER* 1.3 63.3 + - - +
93A ALA* 3.8 0.7 - - - +
94A ARG* 3.0 54.7 + - - +
100A VAL* 4.3 15.3 - - + -
102B LEU* 3.7 29.3 - - + +
103B ALA* 3.3 10.4 - - - +
104B ASN* 3.2 44.5 + - + +
111B ARG* 4.5 2.8 + - - -
118B GLN* 5.9 0.7 + - - -
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Residues in contact with SER 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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87A SER* 3.0 19.0 + - - -
88A GLY* 3.8 6.7 - - - -
90A GLU* 1.3 82.0 + - - +
92A GLU* 1.3 64.0 + - - +
94A ARG* 3.7 6.0 + - - +
95A HIS* 3.1 23.9 + - - +
305A GLN* 6.3 1.6 - - - -
111B ARG* 5.1 11.8 + - - +
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Residues in contact with GLU 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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88A GLY 3.1 18.5 + - - +
89A VAL 3.9 2.7 - - - +
91A SER* 1.3 77.7 - - - +
93A ALA* 1.3 60.5 + - - +
95A HIS* 3.4 15.9 + - - +
96A LYS* 2.9 63.1 + - - +
305A GLN* 3.3 48.6 + - + +
308A MET* 3.8 13.5 - - + -
309A ARG* 3.4 25.3 + - + +
312A ILE* 4.5 0.9 - - + -
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Residues in contact with ALA 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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89A VAL 2.9 16.8 + - - +
90A GLU 3.8 2.0 - - - +
92A GLU* 1.3 75.4 - - - +
94A ARG* 1.3 54.6 + - - +
96A LYS 3.0 4.5 + - - -
97A GLY 2.9 9.2 + - - -
98A TYR* 2.7 52.1 + - + +
100A VAL* 3.6 23.1 - - + -
308A MET* 3.8 15.8 - - + +
312A ILE* 4.9 2.7 - - - -
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Residues in contact with ARG 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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90A GLU* 3.0 35.7 + - - +
91A SER* 3.8 6.1 - - - +
93A ALA* 1.3 77.5 - - - +
95A HIS* 1.3 57.4 + - - +
97A GLY* 2.9 20.0 + - - +
98A TYR 3.6 7.1 + - - +
103B ALA* 5.0 0.6 - - - +
104B ASN 3.3 25.7 + - - +
105B THR* 4.2 1.8 - - - +
111B ARG* 2.2 67.6 + - - +
114B GLU* 3.7 10.8 + - - +
115B ALA* 3.2 24.6 - - - +
118B GLN* 4.4 20.8 + - - +
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Residues in contact with HIS 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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91A SER 3.1 16.0 + - - +
92A GLU* 3.6 16.5 + - - +
93A ALA 3.4 0.2 - - - -
94A ARG* 1.3 77.9 - - - +
96A LYS* 1.3 77.8 + - + +
97A GLY 3.5 0.2 - - - -
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Residues in contact with LYS 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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68A ASN* 4.6 2.3 + - - -
92A GLU* 2.9 38.3 + - - +
93A ALA 3.0 6.5 + - - +
94A ARG 3.0 0.8 - - - -
95A HIS* 1.3 98.4 - - + +
97A GLY* 1.3 60.0 + - - +
98A TYR* 3.5 14.7 + - + -
309A ARG* 4.0 16.0 + - - +
312A ILE* 3.6 40.3 - - + +
313A HIS* 5.7 6.5 + - - -
316A GLU* 5.4 2.0 - - - +
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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