Contacts of the helix formed by residues 77 - 95 (chain A) in PDB entry 4HYJ
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 PHE 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 5.3 0.4 - - - +
75A ASP* 5.1 4.7 - - - -
76A GLY* 1.3 86.0 - - - -
78A PRO* 1.3 64.4 - - - +
79A THR 3.3 2.5 - - - -
80A GLU* 3.3 20.6 + - + +
81A ILE* 3.0 34.4 + - + +
305A LFA 5.2 9.6 - - + -
42B SER* 5.5 13.7 - - - -
309B LFA 3.7 46.7 - - + -
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Residues in contact with PRO 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET* 3.8 36.5 - - + +
64A ALA* 4.2 7.0 - - + -
74A ILE* 6.0 3.8 - - + -
75A ASP 3.5 12.8 - - - +
76A GLY 3.3 10.1 - - - +
77A PHE* 1.3 90.0 - - - +
79A THR* 1.3 67.2 + - - +
81A ILE* 3.7 4.4 - - + +
82A ARG* 3.0 27.3 + - - +
214A GLU* 6.2 2.5 - - + -
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE 3.3 0.8 - - - -
78A PRO* 1.3 84.1 - - - +
80A GLU* 1.3 69.3 + - - +
82A ARG* 3.4 13.0 + - - +
83A TYR* 3.0 52.3 + - + -
127A TYR* 4.4 12.1 - - + -
130A GLU* 4.1 16.2 + - + +
131A SER* 4.9 2.7 - - - +
134A ASN* 3.1 30.4 + - - +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.3 29.4 + - + +
79A THR* 1.3 76.8 + - - +
81A ILE* 1.3 68.4 + - - +
83A TYR* 4.1 1.1 - - - +
84A ILE* 2.9 42.0 + - + +
127A TYR* 2.7 33.5 + - + +
131A SER* 4.6 1.4 + - - -
305A LFA 4.8 7.0 - - + -
109B ARG* 4.3 1.6 + - - -
309B LFA 3.6 59.6 - - + +
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS* 3.3 40.6 - - + +
60A PHE* 4.2 30.3 - - + +
61A MET* 4.3 6.5 - - - -
64A ALA* 5.5 3.4 - - + -
77A PHE* 3.0 30.0 + - + +
78A PRO* 3.7 9.6 - - + +
79A THR 3.3 0.2 - - - -
80A GLU* 1.3 75.6 - - - +
82A ARG* 1.3 62.2 + - - +
84A ILE* 4.0 2.1 - - - +
85A ASP* 3.2 20.8 + - - +
305A LFA 4.1 41.9 - - + +
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS* 3.9 24.5 - - + +
61A MET* 6.1 0.2 - - - -
78A PRO 3.0 17.0 + - - +
79A THR* 3.8 15.0 + - - +
81A ILE* 1.3 78.9 - - - +
83A TYR* 1.3 70.2 + - - +
85A ASP* 3.3 2.6 + - - +
86A TRP* 2.8 82.0 + - + +
130A GLU* 2.9 42.8 + - - -
213A ARG* 3.5 10.3 - - - +
214A GLU* 3.6 32.1 + - - -
217A TYR* 3.8 10.7 - - - -
221A ASP* 6.1 0.4 - - - -
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.0 36.7 + - + +
80A GLU 3.3 2.0 + - - +
82A ARG* 1.3 87.5 - - - +
84A ILE* 1.3 56.2 + - - +
86A TRP* 3.5 23.0 - + - +
87A LEU* 2.7 36.1 + - - +
123A ILE* 3.3 30.6 - - + +
126A GLY* 3.3 19.9 + - - -
127A TYR* 3.3 39.7 - + + -
130A GLU* 2.8 39.3 + - + +
301A RET 3.5 17.1 - - + +
309B LFA 4.5 8.6 - - + +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 2.9 26.1 + - + +
81A ILE 4.0 2.7 - - - +
83A TYR* 1.3 72.9 - - - +
85A ASP* 1.3 67.0 + - - +
87A LEU* 3.4 7.6 + - + +
88A VAL* 3.2 22.7 + - - +
305A LFA 3.7 44.0 - - + -
49B LEU* 4.0 19.5 - - + -
88B VAL* 4.1 21.8 - - + -
92B LEU* 4.0 24.2 - - + -
309B LFA 4.2 23.1 - - + -
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Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 4.1 11.9 - - + -
54A ALA* 3.5 17.6 - - - +
57A HIS* 2.6 44.0 + - + +
58A TYR* 5.1 0.3 - - - -
81A ILE 3.2 11.0 + - - +
82A ARG 3.3 9.0 - - - +
84A ILE* 1.3 77.3 - - - +
86A TRP* 1.3 59.3 + - - +
88A VAL* 3.0 4.0 + - - +
89A THR* 2.8 55.5 + - - +
221A ASP* 5.1 1.2 - - - +
225A LYS* 3.8 8.1 + - - -
305A LFA 4.4 2.6 - - + +
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS* 5.2 1.0 - - - -
82A ARG* 2.8 72.1 + - + +
83A TYR* 3.5 28.5 - + - +
85A ASP* 1.3 80.2 - - - +
87A LEU* 1.3 60.5 + - - +
89A THR* 3.8 4.5 - - - -
90A THR* 2.8 35.0 + - + -
123A ILE* 4.0 15.0 - - + -
130A GLU* 4.8 0.2 - - - -
194A TYR* 3.5 31.4 - + + -
217A TYR* 3.6 15.0 - + - -
221A ASP* 4.5 9.3 + - - -
225A LYS* 4.7 0.2 - - - +
301A RET 3.7 67.7 - - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR 2.7 20.8 + - - +
84A ILE* 3.7 7.9 - - + +
85A ASP 3.2 0.4 + - - -
86A TRP* 1.3 73.2 - - - +
88A VAL* 1.3 58.1 + - - +
90A THR* 4.7 0.9 - - - -
91A PRO* 3.1 24.3 - - - +
119A ASP* 4.9 0.8 - - - +
120A VAL* 4.8 6.5 - - + -
123A ILE* 3.9 16.2 - - + -
124A VAL* 4.2 22.9 - - + -
87B LEU* 3.7 53.9 - - + +
88B VAL* 4.2 20.2 - - + -
91B PRO* 5.1 5.6 - - + -
120B VAL* 5.9 0.4 - - + -
309B LFA 4.3 19.7 - - + -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 4.2 12.3 - - + -
84A ILE* 3.2 13.4 + - + +
85A ASP 3.0 6.1 + - - +
87A LEU* 1.3 80.5 - - - +
89A THR* 1.3 61.3 + - - +
91A PRO* 3.1 14.4 - - - +
92A LEU* 3.4 32.9 - - + +
304A LFA 5.4 0.9 - - + -
305A LFA 3.6 41.7 - - + -
84B ILE* 4.1 16.8 - - + +
88B VAL* 4.2 26.2 - - + -
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Residues in contact with THR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.7 33.6 - - + +
53A VAL* 3.7 23.6 - - + -
85A ASP* 2.8 44.6 + - - +
86A TRP* 3.8 3.3 - - - -
88A VAL* 1.3 73.8 - - + +
90A THR* 1.3 61.7 + - - +
92A LEU* 3.1 2.3 + - - +
93A LEU* 2.8 32.9 + - - +
225A LYS* 3.4 24.0 + - - -
301A RET 3.9 1.6 - - - +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP 2.8 23.6 + - - +
89A THR* 1.3 75.3 + - - +
91A PRO* 1.3 59.9 - - - +
93A LEU* 3.3 8.5 + - - +
94A LEU* 2.9 32.1 + - - +
119A ASP* 2.5 39.3 + - - +
123A ILE* 3.5 14.0 - - + +
191A TRP* 3.9 10.7 - - + -
301A RET 3.8 42.6 - - + -
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Residues in contact with PRO 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 3.1 28.0 - - - +
88A VAL 3.1 8.5 - - - +
90A THR* 1.3 96.2 - - - +
92A LEU* 1.3 56.2 + - - +
94A LEU* 3.2 8.0 + - + +
95A VAL* 3.0 35.0 + - - +
116A VAL* 4.5 18.6 - - + +
119A ASP* 3.5 13.9 - - + +
120A VAL* 5.1 4.5 - - + -
84B ILE* 4.0 18.6 - - + -
87B LEU* 4.6 7.6 - - + -
302B LFA 4.5 7.9 - - + -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.4 31.7 - - + +
49A LEU* 3.7 35.9 - - + -
50A VAL* 3.5 24.9 - - + +
53A VAL* 5.5 0.2 - - + -
88A VAL* 3.4 32.8 - - + +
89A THR* 3.1 3.9 + - - +
91A PRO* 1.3 81.3 - - - +
93A LEU* 1.3 62.0 + - - +
95A VAL* 3.9 7.3 + - - +
96A LYS* 3.8 6.9 + - - +
304A LFA 4.7 3.4 - - + -
84B ILE* 4.8 9.0 - - + -
302B LFA 3.6 39.0 - - + -
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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
----------------------------------------------------------
47A ALA* 6.4 1.1 - - - -
50A VAL* 4.1 21.8 - - + -
89A THR 2.8 26.0 + - - +
90A THR* 3.5 4.9 - - - +
92A LEU* 1.3 76.5 - - - +
94A LEU* 1.3 65.9 + - - +
96A LYS* 3.1 23.8 + - + +
97A PHE* 4.5 0.3 + - - -
191A TRP* 4.1 15.3 - - + -
224A ASN 3.4 26.5 - - - +
225A LYS* 4.2 9.2 - - + +
228A PHE* 3.4 33.7 - - + -
229A GLY* 6.1 0.2 - - - -
301A RET 4.1 32.5 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR 2.9 15.3 + - - +
91A PRO* 3.2 6.7 + - + +
93A LEU* 1.3 77.1 - - - +
95A VAL* 1.3 62.3 + - + +
97A PHE* 3.1 30.7 + - + +
98A PRO* 3.3 8.5 - - - +
112A LEU* 5.3 0.4 - - - -
115A LEU* 3.9 33.7 - - + +
116A VAL* 5.3 2.5 - - + -
119A ASP* 3.5 42.0 - - + +
157A ILE* 4.1 23.1 - - + -
161A LEU* 4.9 0.9 - - + -
187A ILE* 4.0 18.6 - - + -
191A TRP* 3.9 17.7 - - + -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 5.5 4.5 - - + -
91A PRO 3.0 18.7 + - - +
92A LEU* 4.2 7.2 - - - +
93A LEU 3.3 0.6 - - - -
94A LEU* 1.3 75.8 - - - +
96A LYS* 1.3 62.4 + - - +
97A PHE 3.0 0.7 + - - -
98A PRO* 3.0 12.3 - - + +
99A LEU* 2.9 34.9 + - + +
112A LEU* 3.5 35.9 - - + -
116A VAL* 4.9 0.2 - - + -
302B LFA 3.5 44.6 - - + -
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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
------------------------------------------------------------
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