Contacts of the strand formed by residues 0 - 9 (chain D) 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 PHE 0 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1D GLU* 1.3 97.1 + - + +
1D MET* 1.3 64.5 + - - +
53D ASP* 3.8 1.4 - - - +
54D LEU* 2.8 37.7 + - + +
97D LEU* 5.1 2.7 - - + -
123D TYR* 3.2 44.9 - + + +
124D THR 3.4 19.7 - - - -
125D ALA* 4.1 8.3 - - + -
111F GLN* 4.0 27.6 + - + +
112F PRO* 3.5 39.9 - - + -
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Residues in contact with MET 1 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0D PHE* 1.3 79.6 - - - +
2D LEU* 1.3 62.5 + - - +
3D ARG* 3.8 4.6 + - + +
51D GLU* 3.2 38.6 - - + +
52D TRP 3.1 9.4 - - - +
53D ASP* 3.5 25.1 - - - +
54D LEU* 4.1 6.5 - - - +
122D SER 3.8 0.3 - - - +
123D TYR* 3.7 5.4 - - - -
124D THR* 2.8 53.2 + - + +
125D ALA 4.6 0.7 - - - +
126D ALA* 3.7 35.0 - - + +
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Residues in contact with LEU 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 1.3 71.1 - - - +
3D ARG* 1.3 58.7 + - - +
4D VAL* 4.1 16.8 - - + -
28D PHE* 3.7 35.2 - - + -
51D GLU* 3.3 4.0 - - - -
52D TRP* 2.8 56.7 + - + +
54D LEU* 4.0 15.0 - - + +
59D LEU* 4.2 25.4 - - + -
65D LEU* 4.7 4.0 - - + -
88D LEU* 4.6 7.6 - - + -
91D VAL* 5.3 1.1 - - + -
121D VAL* 3.6 27.1 - - + -
122D SER 3.7 9.2 - - - +
123D TYR* 5.0 3.1 - - + -
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Residues in contact with ARG 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 3.8 4.3 + - + +
2D LEU* 1.3 73.2 - - - +
4D VAL* 1.3 64.2 + - - +
5D PHE* 3.7 36.7 - - + -
50D PHE 3.3 10.3 - - - +
51D GLU* 4.4 17.5 - - + +
120D GLN* 3.9 2.0 + - - +
121D VAL* 3.3 4.0 - - - +
122D SER* 2.8 62.6 + - - +
124D THR* 3.7 39.2 + - + +
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Residues in contact with VAL 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LEU* 4.1 7.6 - - + -
3D ARG* 1.3 79.9 - - - +
5D PHE* 1.3 68.4 + - - +
6D ILE* 3.9 27.6 - - + -
26D ALA* 5.6 0.2 - - + -
48D GLU 3.7 1.0 - - - +
49D GLY* 3.5 2.1 - - - -
50D PHE* 2.8 42.2 + - + -
52D TRP* 3.6 31.0 - - + -
65D LEU* 3.9 22.7 - - + -
119D LEU* 4.3 5.6 - - + -
120D GLN 3.4 7.2 - - - +
121D VAL* 3.9 20.0 - - + -
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Residues in contact with PHE 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ARG* 3.7 38.8 - - + -
4D VAL* 1.3 73.7 - - - +
6D ILE* 1.3 62.5 - - - +
7D LEU* 3.5 20.1 + - + +
47D ASN* 5.8 2.9 - - - -
48D GLU 3.3 7.0 - - - +
49D GLY* 4.0 21.3 - - - -
119D LEU* 3.1 7.8 - - - +
120D GLN* 2.8 66.2 + - + +
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Residues in contact with ILE 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.9 18.8 - - + -
5D PHE* 1.3 69.0 - - - +
7D LEU* 1.3 60.4 + - - +
24D CYS* 3.8 28.0 - - - -
26D ALA* 4.7 5.8 - - + -
35D THR* 4.0 12.8 - - + -
46D TRP* 3.6 26.7 - - + +
47D ASN 3.1 5.9 + - - -
48D GLU 2.9 30.8 + - - +
50D PHE* 3.5 28.7 - - + -
67D VAL* 4.6 13.7 - - + -
117D LEU* 4.1 11.4 - - + -
118D VAL 4.3 1.8 - - - -
119D LEU* 4.4 9.0 - - + -
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Residues in contact with LEU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 4.1 23.8 - - + +
6D ILE* 1.3 74.3 - - - +
8D TYR* 1.3 81.6 + - + +
45D VAL* 3.6 4.6 - - - +
46D TRP* 2.9 25.6 + - - -
47D ASN* 2.9 30.3 + - - +
118D VAL* 3.0 31.5 + - + +
119D LEU* 4.9 2.7 - - - -
120D GLN* 5.0 9.6 - - + +
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Residues in contact with TYR 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.9 0.6 - - - +
7D LEU* 1.3 94.5 - - + +
9D ALA* 1.3 59.4 + - - +
10D GLU* 3.6 24.9 + - + -
43D ASN* 3.7 18.6 - - - +
44D PRO 3.2 16.4 - - - +
45D VAL* 3.8 18.2 - - + -
46D TRP* 3.9 9.6 - - - -
102D ASN* 5.1 1.7 + - - -
117D LEU* 3.6 3.4 - - - +
118D VAL* 2.8 63.8 + - + +
212D FMT 5.0 3.3 + - - -
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Residues in contact with ALA 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D TYR* 1.3 74.3 - - - +
10D GLU* 1.3 56.7 + - - +
12D VAL* 3.6 22.7 - - + -
43D ASN* 2.6 37.7 + - - -
44D PRO* 3.1 9.6 + - + +
46D TRP* 3.6 21.9 - - + -
69D VAL* 4.9 1.3 - - + -
105D LEU* 4.9 5.6 - - + -
116D SER 3.2 13.9 - - - +
117D LEU* 4.0 7.4 - - + +
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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