Contacts of the strand formed by residues 19 - 24 (chain M) in PDB entry 3QUM
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 VAL 19 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLU* 5.2 7.2 - - - +
11M VAL* 4.5 16.2 - - + -
12M PHE 5.0 1.3 - - - +
13M VAL* 3.5 31.2 - - + -
18M SER* 1.3 77.4 - - - +
20M SER* 1.3 81.5 + - - +
74M ARG* 3.7 4.2 + - - +
75M ILE* 3.3 35.1 + - + +
78M VAL* 4.9 8.2 - - + +
104M VAL* 5.4 5.8 - - + -
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Residues in contact with SER 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASN* 4.1 10.4 + - - -
213A GLU* 4.2 14.2 + - - +
11M VAL* 5.2 5.2 - - - +
19M VAL* 1.3 93.1 - - - +
21M ILE* 1.3 68.7 + - - +
22M SER* 5.3 2.4 + - - -
72M THR* 5.3 4.6 - - - +
73M LEU 3.4 11.9 - - - -
74M ARG* 3.8 31.2 + - - -
75M ILE* 6.3 0.7 - - - -
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Residues in contact with ILE 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M GLN* 4.9 4.7 - - - +
8M ALA* 3.9 16.2 - - + -
11M VAL* 4.5 9.9 - - + -
20M SER* 1.3 81.7 - - - +
22M SER* 1.3 69.2 + - - +
35M TRP* 3.9 13.9 - - + -
72M THR* 3.2 4.7 - - - -
73M LEU* 2.9 66.5 + - + +
75M ILE* 6.3 0.9 - - + -
86M TYR* 4.9 7.2 - - + -
102M THR* 2.8 49.1 - - + +
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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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5M THR 4.1 3.3 - - - +
6M GLN* 3.8 19.1 - - - +
7M THR* 4.9 8.7 + - - +
8M ALA* 5.7 2.3 + - - +
20M SER* 5.3 2.6 + - - -
21M ILE* 1.3 81.8 + - - +
23M CYS* 1.3 60.7 + - - +
24M ARG* 4.4 6.1 + - - -
35M TRP* 4.6 1.8 - - - -
71M PHE 3.7 2.9 - - - -
72M THR* 3.2 21.1 - - - +
102M THR* 5.2 0.5 - - - +
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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 MET* 3.7 19.3 - - - -
5M THR 4.0 4.5 - - - -
6M GLN* 4.6 4.5 - - + -
21M ILE 4.2 0.6 + - - -
22M SER* 1.3 72.0 - - - +
24M ARG* 1.3 61.3 + - - +
33M LEU* 4.4 2.9 - - - -
35M TRP* 3.5 26.2 - - + -
71M PHE* 2.8 49.5 + - + +
88M CYS* 2.1 46.9 - - - -
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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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128B VAL* 5.4 5.5 - - - +
130B GLY 3.9 6.9 + - - -
131B ASP* 2.9 49.5 + - - +
132B THR* 4.1 14.5 - - + +
133B THR* 3.8 20.6 + - - +
4M MET* 4.9 2.2 - - - -
5M THR* 3.3 38.6 + - - +
7M THR* 4.5 23.2 - - - +
22M SER* 5.8 5.1 - - - -
23M CYS* 1.3 74.9 - - - +
25M SER* 1.3 63.9 + - - +
69M THR* 3.2 17.7 - - - +
70M ASP* 3.5 24.4 + - - +
71M PHE* 4.8 0.2 - - - -
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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