Contacts of the strand formed by residues 15 - 20 (chain C) in PDB entry 4M75
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 ARG 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ASN* 5.4 1.4 - - - +
14C GLU* 1.3 76.7 - - - +
16C VAL* 1.3 62.8 + - - +
27C VAL* 3.2 28.2 + - + +
28C GLY* 3.4 13.1 - - - -
29C THR* 3.3 23.5 + - - +
43C ASP* 2.1 40.6 + - - +
44C ALA 5.2 0.2 - - - -
45C VAL* 4.5 9.1 - - - +
78C THR* 4.3 5.9 - - - +
79C PRO* 3.2 30.3 - - + +
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN* 4.1 24.5 - - + +
14C GLU 3.4 14.1 - - - +
15C ARG* 1.3 76.3 - - - +
17C TYR* 1.3 59.5 + - - +
18C ILE* 4.2 13.7 + - + +
27C VAL* 3.8 8.8 - - - +
28C GLY 3.3 28.9 + - - +
30C LEU* 3.9 30.5 - - + -
41C LEU* 4.0 12.3 - - + -
76C ILE* 4.4 9.4 - - + -
77C SER 3.2 14.6 - - - +
79C PRO* 3.8 4.3 - - - -
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Residues in contact with TYR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 1.3 74.8 - - - +
18C ILE* 1.3 61.7 + - - +
19C LYS* 3.5 37.9 - - + -
25C THR* 3.5 30.5 + - + +
26C LEU 3.8 9.6 - - - -
27C VAL* 4.4 9.2 - - + -
49C TYR* 5.4 1.7 + - - -
75C LEU* 3.7 5.1 - - + +
76C ILE* 3.2 5.4 - - - -
77C SER* 2.8 44.5 + - - +
78C THR 4.1 4.3 - - - -
79C PRO* 3.9 26.9 - - + +
65D ASN* 5.0 7.3 + - - -
67D PHE* 4.4 19.8 - + - -
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 4.4 14.8 - - + +
17C TYR* 1.3 79.5 - - - +
19C LYS* 1.3 65.8 + - - +
20C LEU* 4.0 16.3 + - + +
25C THR* 3.5 5.4 - - - +
26C LEU* 3.0 41.9 + - + +
39C ILE* 3.6 40.6 - - + -
41C LEU* 4.6 11.9 - - + -
68C ILE* 4.4 13.7 - - + -
73C VAL* 3.9 24.9 - - + -
75C LEU 3.4 7.4 - - - +
76C ILE* 4.2 7.2 - - + -
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Residues in contact with LYS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A GLY 3.8 20.2 + - - +
163A VAL* 4.6 11.7 - - + -
17C TYR* 3.5 21.5 - - + -
18C ILE* 1.3 74.8 - - - +
20C LEU* 1.3 64.0 + - - +
24C ARG 4.7 1.8 - - - +
25C THR* 3.8 17.5 - - - +
49C TYR* 6.2 1.6 - - + -
73C VAL* 4.2 0.2 - - - -
74C THR* 2.8 41.7 + - + -
75C LEU* 2.9 41.9 + - + +
32D LEU* 3.9 7.3 - - - +
34D TYR* 3.5 7.7 + - - -
54D GLU* 2.9 35.7 + - - -
65D ASN* 4.6 2.4 - - - +
67D PHE* 5.6 2.7 - - - -
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A VAL* 2.3 36.9 - - - +
68B ARG* 5.7 1.1 - - + -
69B TYR* 3.1 17.7 - - + +
18C ILE* 4.0 6.7 - - + +
19C LYS* 1.3 75.5 - - - +
21C ARG* 1.3 57.5 + - - +
22C GLY 3.3 0.5 + - - -
24C ARG* 3.2 27.1 + - + +
25C THR* 4.7 0.4 - - - +
26C LEU* 2.7 40.8 - - + -
68C ILE* 3.8 7.9 - - + -
72C THR* 3.0 33.0 - - - +
73C VAL* 3.7 24.9 - - + +
74C THR* 3.9 2.9 - - - -
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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