Contacts of the strand formed by residues 1 - 10 (chain C) in PDB entry 4IHB
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 MET 1 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0C PHE* 1.3 81.5 - - - +
2C LEU* 1.3 62.4 + - - +
3C ARG 3.4 2.4 + - - -
51C GLU* 3.2 36.6 - - + +
52C TRP 3.1 15.9 - - - +
53C ASP* 4.0 23.8 - - + +
54C LEU* 4.1 5.4 - - - -
123C TYR* 3.6 1.9 - - - -
124C THR* 2.8 41.5 + - - +
125C ALA 5.1 1.6 - - - +
126C ALA* 4.0 37.2 - - + +
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Residues in contact with LEU 2 (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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1C MET* 1.3 69.3 - - - +
3C ARG* 1.3 59.8 + - - +
4C VAL* 4.3 13.9 - - + -
28C PHE* 3.7 41.3 - - + -
51C GLU* 3.4 3.8 - - - -
52C TRP* 2.9 46.1 + - + +
54C LEU* 3.7 18.2 - - + +
65C LEU* 4.9 4.5 - - + -
88C LEU* 4.2 10.5 - - + -
121C VAL* 3.6 28.3 - - + -
122C SER 3.6 7.6 - - - +
123C TYR* 3.9 28.9 - - + +
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Residues in contact with ARG 3 (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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1C MET 3.4 0.4 + - - +
2C LEU* 1.3 74.0 - - - +
4C VAL* 1.3 63.0 + - - +
5C PHE* 3.2 39.5 - - + -
50C PHE 3.4 5.4 - - - +
51C GLU* 3.8 32.1 + - + +
120C GLN* 4.0 2.2 + - - +
121C VAL* 3.4 3.1 - - - -
122C SER* 2.8 64.8 + - - +
124C THR* 3.1 41.2 + - - +
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Residues in contact with VAL 4 (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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2C LEU* 4.3 8.7 - - + -
3C ARG* 1.3 79.9 - - - +
5C PHE* 1.3 72.4 + - - +
6C ILE* 4.1 16.2 - - + -
26C ALA* 5.9 1.1 - - + -
48C GLU 3.8 0.7 - - - +
49C GLY* 3.3 2.1 - - - -
50C PHE* 2.7 43.8 + - + +
52C TRP* 3.7 28.3 - - + -
65C LEU* 3.8 30.7 - - + -
119C LEU* 4.2 7.2 - - + -
120C GLN 3.4 7.4 - - - +
121C VAL* 3.9 15.0 - - + -
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Residues in contact with PHE 5 (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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3C ARG* 3.2 38.4 - - + -
4C VAL* 1.3 73.2 - - - +
6C ILE* 1.3 62.4 + - - +
7C LEU* 3.6 20.4 + - + +
47C ASN* 5.7 3.4 - - - -
48C GLU 3.4 5.4 - - - +
49C GLY* 3.6 25.1 - - - -
119C LEU* 3.2 6.8 - - - +
120C GLN* 2.9 63.2 + - + +
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Residues in contact with ILE 6 (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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4C VAL* 4.1 12.8 - - + -
5C PHE* 1.3 73.9 - - - +
7C LEU* 1.3 60.4 + - - +
24C CYS* 3.8 32.5 - - + +
26C ALA* 4.2 18.8 - - + -
33C LYS 6.1 0.2 - - - +
35C THR* 3.9 8.7 - - + -
46C TRP* 3.6 27.6 - - + +
47C ASN 3.1 18.0 + - - -
48C GLU 2.9 17.7 + - - +
50C PHE* 3.7 25.1 - - + -
67C VAL* 4.7 7.6 - - + -
117C LEU* 4.0 12.6 - - + -
118C VAL 4.6 0.2 - - - +
119C LEU* 4.2 9.6 - - + -
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Residues in contact with LEU 7 (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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5C PHE* 4.1 24.9 - - + +
6C ILE* 1.3 74.3 - - - +
8C TYR* 1.3 79.8 + - + +
45C VAL* 3.6 4.6 - - - +
46C TRP* 2.9 26.7 + - - -
47C ASN* 2.9 30.2 + - + +
118C VAL* 3.0 31.7 + - + +
119C LEU* 4.7 4.3 - - - -
120C GLN* 5.3 5.8 - - + +
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Residues in contact with TYR 8 (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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7C LEU* 1.3 95.6 - - + +
9C ALA* 1.3 64.7 + - - +
10C GLU* 3.7 37.2 + - + -
43C ASN* 6.2 0.4 - - + -
44C PRO 3.2 15.5 - - - +
45C VAL* 3.8 21.5 - - + -
46C TRP* 3.6 9.8 - - - -
102C ASN* 5.1 2.4 + - - -
117C LEU* 3.5 2.1 - - - +
118C VAL* 2.8 64.4 + - + +
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Residues in contact with ALA 9 (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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8C TYR* 1.3 77.2 - - - +
10C GLU* 1.3 66.4 + - - +
12C VAL* 3.6 20.2 - - + -
43C ASN* 3.3 25.6 - - - +
44C PRO* 3.0 9.2 + - + +
46C TRP* 3.4 25.0 - - + -
69C VAL* 5.1 1.1 - - + -
105C LEU* 4.9 4.7 - - + -
116C SER 3.2 13.0 - - - +
117C LEU* 4.1 7.6 - - + -
118C VAL 4.8 0.2 - - - +
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Residues in contact with GLU 10 (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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95B PRO* 5.9 0.5 - - - +
8C TYR* 3.7 28.9 + - + -
9C ALA* 1.3 76.6 - - - +
11C ASN* 1.3 83.3 + - - +
12C VAL* 3.4 3.0 - - - +
43C ASN* 3.5 14.9 - - + +
102C ASN* 5.1 7.3 + - - -
115C ALA* 3.2 2.9 - - - +
116C SER* 2.9 43.6 + - - +
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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
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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