Contacts of the strand formed by residues 77 - 82 (chain M) in PDB entry 3INU
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 SER 77 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21M SER* 6.3 0.2 - - - -
22M CYS 3.1 10.1 + - - -
23M ALA* 4.3 8.1 - - - +
29M LEU* 3.2 10.9 - - - +
71M ARG* 3.8 0.2 - - - -
72M ASP 3.0 31.3 + - - -
75M GLU* 3.1 19.8 + - - +
76M ASN* 1.3 75.6 + - - +
78M LEU* 1.3 61.6 + - - +
79M TYR* 3.3 29.8 + - - -
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Residues in contact with LEU 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M LEU* 6.2 0.2 - - + -
21M SER* 3.4 4.0 - - - -
22M CYS* 2.8 41.1 + - + +
29M LEU* 4.1 11.0 - - + +
34M MET* 3.7 36.8 - - + -
35M ASN 3.9 13.2 - - - +
36M TRP* 3.5 32.0 - - + +
51M ILE* 3.7 16.6 - - + -
69M ILE* 4.2 2.0 - - + -
70M SER 3.2 24.5 - - - +
71M ARG* 4.6 4.0 - - + -
77M SER* 1.3 74.3 - - - +
79M TYR* 1.3 66.5 + - - +
92M CYS* 3.9 14.1 - - + -
93M VAL 5.2 0.2 - - - +
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Residues in contact with TYR 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ARG* 3.5 44.3 + - + +
20M LEU 3.3 6.5 - - - +
21M SER* 3.7 18.2 - - - -
36M TRP* 3.4 13.9 + - - -
69M ILE* 3.5 1.7 - - - +
70M SER* 3.0 57.2 + - - +
71M ARG 4.2 2.0 - - - -
72M ASP* 3.8 30.8 + - + +
75M GLU* 5.0 3.3 - - - +
77M SER* 3.3 29.7 + - - -
78M LEU* 1.3 80.9 - - - +
80M LEU* 1.3 60.7 + - - +
81M GLN* 4.2 0.9 - - + +
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Residues in contact with LEU 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M LEU 3.8 0.3 - - - +
19M ARG* 3.4 3.4 - - - -
20M LEU* 2.8 42.4 + - + +
36M TRP* 3.5 43.7 - - + -
48M VAL* 4.3 3.4 - - + -
49M SER* 4.8 5.8 - - - -
67M PHE* 3.9 34.1 - - + -
68M THR 3.8 18.2 - - - +
69M ILE* 4.0 12.6 - - + +
79M TYR* 1.3 74.8 - - - +
81M GLN* 1.3 62.1 + - - +
82M MET* 3.7 15.0 + - + +
90M TYR* 4.2 17.5 - - + -
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Residues in contact with GLN 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M SER* 5.5 2.5 - - - -
18M LEU 3.6 7.2 - - - +
19M ARG* 4.3 16.1 - - + +
66M ARG 3.8 1.2 - - - +
67M PHE* 3.3 2.8 - - - -
68M THR* 2.8 54.3 + - + +
70M SER* 6.2 1.3 - - - -
79M TYR* 4.2 1.0 - - + +
80M LEU* 1.3 70.7 - - - +
82M MET* 1.3 95.3 + - + +
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Residues in contact with MET 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M GLY 3.8 0.5 - - - +
17M SER* 2.9 7.4 + - - -
18M LEU* 2.7 45.1 + - + +
20M LEU* 3.1 49.1 - - + -
66M ARG 3.9 2.7 - - - -
67M PHE* 3.6 37.2 - - + -
80M LEU* 3.7 10.1 + - + +
81M GLN* 1.3 71.6 - - - +
82M ASN* 1.3 88.0 + - - +
90M TYR* 3.9 17.9 - - - -
109M VAL* 4.1 14.4 - - + -
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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