Contacts of the strand formed by residues 74 - 81 (chain B) in PDB entry 4H3I
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 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLY* 3.5 5.2 - - - -
70B LYS 2.6 34.2 + - - +
71B SER 3.5 4.7 + - - -
73B GLN* 1.3 78.9 - - - +
75B TYR* 1.3 65.9 + - - -
76B TYR* 4.3 3.3 + - - -
91B LEU* 3.6 12.1 - - - -
290B SER 5.2 2.0 - - - -
503B 10V 3.8 19.2 - - - -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 4.6 10.3 - - + -
68B ARG 3.3 14.8 - - - +
69B GLY 3.7 17.0 - - - -
70B LYS* 3.6 8.2 - - - -
71B SER* 3.4 23.1 + - - -
74B GLY* 1.3 77.9 - - - -
76B TYR* 1.3 54.4 + - - +
91B LEU* 3.4 6.9 - - - +
92B VAL* 2.8 39.7 + - + +
215B LEU* 4.0 44.6 - - + -
216B CYS 3.3 17.2 + - - -
217B GLY* 3.7 1.0 + - - -
232B GLY 3.2 30.7 - - - -
290B SER* 5.2 6.8 + - - +
396B ALA* 4.6 4.7 - - + -
400B GLU* 2.5 27.7 + - - -
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN 4.0 0.5 - - - +
67B LEU* 3.4 10.1 - - - -
68B ARG* 2.9 81.3 + - + +
69B GLY* 4.2 7.4 - - - -
73B GLN* 6.1 0.9 - - - -
74B GLY 4.7 2.5 - - - -
75B TYR* 1.3 75.7 - - - +
77B VAL* 1.3 61.6 + - - +
89B ASN* 3.5 37.9 - - + -
90B ILE 3.1 24.5 - - - +
91B LEU* 3.7 4.3 - - - +
92B VAL* 4.2 1.1 - - - +
175B ASN* 3.0 39.9 + - + +
176B TRP* 4.2 19.5 - + + -
227B VAL* 4.7 4.2 + - + +
228B LEU* 4.2 4.9 - - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN* 3.8 32.3 - - + +
67B LEU* 3.8 7.4 - - + -
76B TYR* 1.3 74.5 - - - +
78B GLU* 1.3 70.9 + - - +
79B MET* 3.7 21.7 + - + -
89B ASN* 4.6 4.3 - - - -
90B ILE* 2.7 38.2 + - + +
92B VAL* 4.0 4.7 - - + +
148B ILE* 4.2 9.9 - - + -
150B HIS* 5.2 2.0 - - + +
180B LEU* 4.9 2.7 - - + -
235B MET* 3.6 33.4 - - + -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN 4.5 3.0 + - - -
68B ARG* 5.4 1.8 + - - +
77B VAL* 1.3 79.1 - - - +
79B MET* 1.3 68.3 + - - +
87B THR* 3.6 31.7 + - + +
88B LEU 3.6 5.6 - - - +
89B ASN* 4.0 15.5 + - - +
111B ARG* 5.1 0.3 + - - -
148B ILE* 3.8 11.3 - - - +
149B PRO* 3.3 40.8 - - + +
150B HIS* 4.4 21.0 + - + -
502B TLA 5.0 4.9 - - - +
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Residues in contact with MET 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 4.0 10.3 - - + -
78B GLU* 1.3 80.6 - - - +
80B THR* 1.3 68.3 + - - +
81B VAL* 5.4 1.3 - - + -
87B THR* 3.5 6.1 - - - +
88B LEU* 2.9 31.5 + - + -
90B ILE* 3.5 43.1 - - + -
99B PHE* 3.9 16.6 - - + -
146B VAL* 3.6 26.7 - - + -
147B SER 3.4 7.4 - - - +
148B ILE* 4.0 13.2 - - + -
149B PRO* 3.9 1.3 - - - -
180B LEU* 4.1 18.2 - - + -
197B PHE* 4.0 22.0 - - + -
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B MET* 1.3 80.2 - - - +
81B VAL* 1.3 63.2 + - - +
82B GLY 5.5 0.4 + - - -
85B PRO* 4.0 25.1 - - + +
86B GLN 3.2 7.4 - - - -
87B THR* 3.9 17.9 - - - +
145B LEU 3.9 0.8 - - - +
146B VAL* 3.3 8.8 - - - +
147B SER* 3.0 45.7 + - - -
149B PRO* 3.7 21.8 - - + -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 5.4 2.2 - - + -
80B THR* 1.3 80.8 - - - +
82B GLY* 1.3 62.3 + - - +
86B GLN* 2.8 44.5 + - + +
88B LEU* 4.1 18.6 - - + -
90B ILE* 6.4 0.4 - - + -
99B PHE* 3.9 29.2 - - + -
101B VAL* 5.2 2.2 - - + -
113B TYR* 3.5 31.9 - - + -
145B LEU 3.5 4.9 - - - -
146B VAL* 4.2 3.8 - - + -
160B ILE* 4.0 21.5 - - + -
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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