Contacts of the strand formed by residues 74 - 81 (chain A) in PDB entry 4R95
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG 4.0 0.2 - - - +
69A GLY* 3.4 7.1 - - - -
70A LYS 2.7 29.3 + - - -
71A SER 4.0 4.8 + - - -
72A GLY 3.7 1.2 - - - -
73A GLN* 1.3 82.6 - - - +
75A TYR* 1.3 60.8 + - - -
76A TYR* 4.1 4.9 + - - -
91A LEU* 3.7 17.3 - - - -
174A SER 5.3 0.7 - - - +
176A TRP* 4.7 2.3 - - - -
290A SER 5.4 5.4 - - - -
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.5 9.0 - - + -
68A ARG 3.3 15.0 - - - -
69A GLY 3.4 17.6 + - - -
70A LYS* 3.6 11.4 - - - +
71A SER* 3.5 21.3 - - - -
74A GLY* 1.3 77.2 - - - -
76A TYR* 1.3 59.5 + - - +
91A LEU* 3.3 5.4 - - - +
92A VAL* 2.8 32.9 + - + +
215A LEU* 3.8 42.4 - - + -
216A CYS 3.2 25.0 + - - -
217A GLY* 3.5 2.3 + - - -
232A GLY 3.1 30.5 - - - -
290A SER* 5.4 6.2 + - - +
396A ALA* 4.5 4.5 - - + -
400A GLU* 2.6 25.5 + - - -
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 3.9 0.3 - - - +
67A LEU* 3.3 9.7 - - - -
68A ARG* 2.9 80.3 + - + +
69A GLY* 4.0 7.1 + - - -
74A GLY 4.2 4.0 - - - -
75A TYR* 1.3 75.5 - - - +
77A VAL* 1.3 60.7 + - - +
78A GLU 5.2 0.4 - - - -
89A ASN* 3.5 36.1 - - + -
90A ILE 3.2 22.0 - - - +
91A LEU* 3.7 3.4 - - - +
174A SER 3.3 24.7 - - - -
175A ASN* 2.9 27.1 + - + +
176A TRP* 3.9 20.0 - + + -
227A VAL* 4.8 3.0 + - + -
228A LEU* 4.3 3.8 - - - +
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN* 3.7 37.2 - - + +
67A LEU* 3.6 11.4 - - + -
76A TYR* 1.3 75.2 - - - +
78A GLU* 1.3 72.6 + - - +
79A MET* 3.6 20.3 + - + -
89A ASN* 4.5 2.9 - - - -
90A ILE* 2.8 39.0 + - - +
92A VAL* 3.8 6.0 - - + +
148A ILE* 4.1 10.1 - - + -
150A HIS* 5.1 1.1 - - + +
180A LEU* 5.0 2.5 - - + -
235A MET* 3.7 24.9 - - + -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 4.5 3.2 + - - -
68A ARG* 5.5 2.1 + - - -
76A TYR* 5.2 0.2 - - - -
77A VAL* 1.3 78.0 - - - +
79A MET* 1.3 67.6 + - - +
87A THR* 3.5 32.5 + - + +
88A LEU 3.6 6.1 - - - +
89A ASN* 3.8 14.5 + - - +
148A ILE* 3.7 12.5 - - - +
149A PRO* 3.4 38.3 - - + +
150A HIS* 4.2 20.5 + - + -
502A TLA 4.9 6.4 - - - +
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Residues in contact with MET 79 (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 VAL* 4.0 9.6 - - + +
78A GLU* 1.3 79.1 - - - +
80A THR* 1.3 67.9 + - - +
81A VAL* 5.4 1.3 - - + -
87A THR* 3.5 5.4 - - - +
88A LEU* 2.9 32.9 + - + -
90A ILE* 3.7 43.5 - - + -
99A PHE* 3.9 13.9 - - + -
146A VAL* 3.6 26.7 - - + -
147A SER 3.4 8.7 - - - +
148A ILE* 3.8 23.1 - - + -
149A PRO* 3.8 2.2 - - - -
180A LEU* 4.0 18.4 - - + -
197A PHE* 4.0 14.4 - - + -
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Residues in contact with THR 80 (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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78A GLU* 5.5 0.2 - - - +
79A MET* 1.3 77.0 - - - +
81A VAL* 1.3 68.7 + - - +
85A PRO* 3.6 28.4 - - + +
86A GLN 3.2 6.3 - - - -
87A THR* 3.9 20.0 - - + +
145A LEU 4.6 0.7 - - - -
146A VAL* 3.4 4.2 - - - +
147A SER* 3.0 50.7 + - - +
149A PRO* 3.7 21.1 - - + -
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Residues in contact with VAL 81 (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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79A MET* 5.4 2.2 - - + -
80A THR* 1.3 81.4 - - - +
82A GLY* 1.3 61.7 + - - +
86A GLN* 2.8 39.0 + - + +
88A LEU* 3.7 25.4 - - + -
90A ILE* 6.3 0.2 - - + -
99A PHE* 3.7 36.1 - - + -
101A VAL* 5.4 1.8 - - + -
113A TYR* 3.4 30.5 - - + -
144A ASP* 4.6 0.2 - - - -
145A LEU 3.4 5.4 - - - -
146A VAL* 4.1 3.1 - - + -
160A ILE* 3.9 16.4 - - + -
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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
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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