Contacts of the strand formed by residues 19 - 25 (chain M) in PDB entry 3H3P
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 ALA 19 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11M GLN* 3.5 12.3 - - - +
13M LEU* 3.5 24.2 - - + -
17M GLU 4.1 1.0 + - - -
18M ARG* 1.3 74.6 - - - +
20M THR* 1.3 61.5 + - - +
21M LEU* 3.9 10.0 - - + +
74M LEU 3.7 0.3 - - - +
75M THR* 3.4 6.9 - - - +
76M ILE* 2.9 44.0 + - + +
79M LEU* 4.3 10.3 - - + -
105M VAL* 5.0 4.9 - - + -
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Residues in contact with THR 20 (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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8M PRO* 4.4 4.3 - - - +
11M GLN* 3.5 19.3 + - - +
18M ARG* 3.9 22.2 + - - -
19M ALA* 1.3 74.5 + - - +
21M LEU* 1.3 64.6 + - - +
22M SER* 4.2 7.1 + - - +
73M THR* 3.9 22.7 - - + -
74M LEU 3.5 3.6 - - - -
75M THR* 4.1 6.6 + - - +
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Residues in contact with LEU 21 (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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6M GLN* 5.7 0.2 - - - +
7M SER 4.0 5.2 - - - +
8M PRO* 5.2 0.7 - - - -
11M GLN* 3.4 21.1 - - - +
19M ALA* 3.9 10.8 - - + -
20M THR* 1.3 85.6 - - - +
22M SER* 1.3 61.7 + - - +
36M TRP* 4.3 10.1 - - + -
73M THR* 3.3 8.7 - - - +
74M LEU* 2.9 57.8 + - + +
76M ILE* 5.3 4.0 - - + -
87M TYR* 3.6 39.5 - - + -
103M THR* 4.5 20.6 - - + +
105M VAL* 4.5 7.0 - - + -
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Residues in contact with SER 22 (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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6M GLN* 3.2 9.2 + - - +
7M SER* 3.0 52.0 + - - +
8M PRO* 5.5 0.3 - - - +
20M THR* 4.6 8.7 + - - +
21M LEU* 1.3 78.3 + - - +
23M CYS* 1.3 61.0 + - - +
24M ARG* 4.2 1.1 - - - -
36M TRP* 4.0 3.8 - - - -
71M ASP* 5.9 4.7 - - - -
72M PHE 3.4 6.3 - - - -
73M THR* 4.7 3.5 + - - +
103M THR* 5.0 0.2 + - - -
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Residues in contact with CYS 23 (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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4M LEU* 3.6 24.5 - - - -
5M THR 4.0 2.2 - - - -
6M GLN* 4.4 1.3 - - - +
22M SER* 1.3 74.8 - - - +
24M ARG* 1.3 60.5 + - - +
25M ALA 5.3 0.2 - - - -
34M LEU* 4.1 7.4 - - - -
36M TRP* 3.5 19.2 - - + -
70M THR 3.9 0.3 - - - +
71M ASP* 3.7 2.6 - - - -
72M PHE* 2.8 45.5 + - + +
89M CYS* 2.1 49.8 - - + -
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Residues in contact with ARG 24 (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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3M VAL 3.6 1.6 - - - +
4M LEU* 3.4 5.6 - - - -
5M THR* 2.9 49.9 + - + +
22M SER* 4.2 1.3 - - - -
23M CYS* 1.3 73.1 - - - +
25M ALA* 1.3 68.6 + - - +
70M THR* 3.3 20.2 - - - -
71M ASP* 4.5 15.9 - - - +
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Residues in contact with ALA 25 (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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2M ILE* 4.0 2.5 - - + -
4M LEU* 3.5 24.2 - - + +
23M CYS* 4.2 1.0 + - - -
24M ARG* 1.3 80.0 - - - +
26M SER* 1.3 63.2 + - - +
27M GLN 3.1 19.1 - - - +
29M VAL* 3.8 17.7 - - + -
70M THR* 2.6 38.7 + - - +
72M PHE* 5.2 2.0 - - + -
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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