Contacts of the strand formed by residues 5 - 12 (chain D) in PDB entry 4PP8
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 LEU 5 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D SER* 1.3 72.7 - - - +
6D ARG* 1.3 62.2 + - - +
7D CYS* 3.6 28.0 - - - -
26D CYS* 4.6 2.5 - - + -
27D PHE 3.5 10.3 - - - +
28D VAL* 4.1 17.9 - - + -
33D ILE* 5.2 7.6 - - + -
57D VAL* 4.5 12.3 - - + -
61D LEU* 4.6 6.5 - - + -
96D MET* 3.7 5.6 - - + +
97D ILE* 3.6 1.7 - - - -
98D TYR* 2.8 47.9 + - + +
164D MET* 4.0 37.5 - - + -
167D PHE* 4.8 9.2 - - + -
168D LEU* 4.0 12.5 - - + +
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Residues in contact with ARG 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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3D HIS* 6.2 1.8 - - - -
4D SER* 3.8 11.3 + - - +
5D LEU* 1.3 77.7 - - - +
7D CYS* 1.3 61.2 + - - +
8D ASN* 4.1 13.6 + - - +
25D LYS 3.7 1.4 - - - +
26D CYS* 3.1 1.7 - - - -
27D PHE* 2.7 50.7 + - + +
29D GLY 6.3 1.3 - - - +
95D THR* 3.7 20.6 - - + +
96D MET 3.2 8.1 - - - +
97D ILE* 3.3 39.2 - - + +
111D GLU* 5.1 2.0 + - - -
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Residues in contact with CYS 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 LEU* 3.6 19.5 - - - +
6D ARG* 1.3 72.9 - - - +
8D ASN* 1.3 62.3 + - - +
9D LEU* 3.9 16.9 - - + +
25D LYS 3.5 3.4 - - - -
26D CYS* 2.1 46.0 - - - -
61D LEU* 4.4 4.5 - - - -
65D LEU* 4.4 9.0 - - + -
94D VAL 3.6 1.6 - - - +
95D THR* 3.4 3.6 - - - -
96D MET* 2.8 54.2 + - + +
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Residues in contact with ASN 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 ARG* 4.6 10.7 + - - +
7D CYS* 1.3 75.3 - - - +
9D LEU* 1.3 61.2 + - - +
10D THR* 5.2 2.8 + - - +
23D GLU 3.7 1.2 - - - +
24D ALA* 3.4 3.3 - - - -
25D LYS* 2.8 40.7 + - + +
27D PHE* 3.8 24.2 - - - -
94D VAL 3.4 3.1 - - - +
95D THR* 3.4 34.4 + - - +
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Residues in contact with LEU 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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7D CYS* 3.9 26.9 - - + +
8D ASN* 1.3 80.1 - - - +
10D THR* 1.3 62.2 + - - +
11D ILE* 4.5 9.0 - - + -
23D GLU 3.4 5.8 - - - +
24D ALA* 4.7 8.5 - - + -
65D LEU* 4.3 16.4 - - + -
68D LEU* 3.9 19.5 - - + -
69D CYS* 4.1 19.1 - - - -
72D LEU* 3.9 25.1 - - + -
92D LEU 3.8 0.2 - - - +
93D GLN* 3.3 5.9 - - - +
94D VAL* 2.7 52.5 + - + +
110D TRP* 4.6 7.0 - - + -
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Residues in contact with THR 10 (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 ASN* 5.2 2.1 + - - +
9D LEU* 1.3 75.8 + - - +
11D ILE* 1.3 72.9 + - - +
12D LYS* 4.6 16.4 - - + -
20D LEU* 5.1 2.6 - - + +
22D TYR* 3.1 9.0 - - - +
23D GLU* 2.9 46.6 + - + +
89D TYR* 6.4 0.7 - - + -
91D HIS* 5.1 7.0 - - + -
92D LEU 3.3 8.5 - - - +
93D GLN* 4.7 10.3 - - + +
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Residues in contact with ILE 11 (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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9D LEU* 4.5 3.8 - - + -
10D THR* 1.3 84.6 - - - +
12D LYS* 1.3 66.6 + - - +
21D TRP* 3.3 13.7 - - + +
22D TYR* 4.4 5.6 - - + -
69D CYS* 4.2 28.5 - - - +
72D LEU* 3.9 33.4 - - + -
73D ARG* 4.1 26.7 - - + +
76D VAL* 4.7 13.1 - - + +
91D HIS* 3.4 4.5 - - - +
92D LEU* 2.8 49.0 + - + +
94D VAL* 5.3 0.4 - - + -
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Residues in contact with LYS 12 (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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10D THR* 4.6 10.1 - - + -
11D ILE* 1.3 79.3 - - - +
13D ASP* 1.3 72.9 + - - +
14D PRO* 3.6 0.7 - - - +
15D THR* 5.1 2.0 + - - +
18D ASP* 3.2 43.0 + - - +
20D LEU* 2.7 44.4 + - + +
21D TRP* 2.9 33.8 + - - +
89D TYR* 3.5 30.5 - - + +
90D PRO 4.1 15.3 - - - +
91D HIS* 4.4 6.7 - - + +
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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