Contacts of the strand formed by residues 201 - 210 (chain A) 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 SER 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A HIS* 3.0 20.1 + - - +
199A LYS 3.2 3.3 + - - -
200A THR* 1.3 82.9 + - - +
202A THR* 1.3 65.8 + - - +
203A SER* 3.3 22.8 + - - +
205A ILE* 3.3 33.1 - - - +
27M LEU* 4.5 9.5 - - - -
29M GLY* 3.5 12.5 + - - -
31M THR* 4.3 8.0 - - - +
51M MET* 5.9 0.2 - - - +
67M SER* 5.8 0.2 - - - -
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Residues in contact with THR 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER* 1.3 74.2 - - - +
203A SER* 1.3 65.2 + - - +
204A PRO* 3.9 3.5 - - - +
29M GLY* 3.1 17.4 + - - +
30M ASN* 3.2 18.6 + - - +
16Q ILE* 3.4 53.0 + - + +
17Q VAL* 5.4 0.9 - - - -
21Q GLU* 5.6 0.9 - - - +
154Q LYS* 3.4 30.7 - - - +
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A SER* 3.3 23.3 + - - +
202A THR* 1.3 82.4 + - - +
204A PRO* 1.3 69.9 - - - +
205A ILE* 3.2 4.3 + - - +
31M THR* 3.8 21.5 - - - +
50M ARG 3.6 12.0 + - - -
51M MET* 4.2 10.5 - - - -
52M SER* 2.6 31.1 + - - -
53M ASN* 4.8 2.4 + - - -
67M SER* 6.4 0.2 - - - -
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Residues in contact with PRO 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLU* 4.3 20.0 - - + +
196A ALA 3.5 16.6 - - - +
197A THR* 5.4 3.4 - - - +
202A THR 4.1 3.8 - - - +
203A SER* 1.3 87.9 - - - +
205A ILE* 1.3 63.0 + - - +
206A VAL* 3.3 22.7 + - + +
51M MET* 4.8 1.6 - - - +
52M SER* 4.5 7.6 - - - +
65M SER* 4.5 15.0 + - - +
66M GLY 4.5 3.3 + - - -
67M SER* 4.2 3.6 - - - -
16Q ILE 6.1 0.7 - - - +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PRO* 4.8 26.5 - - + -
114A THR* 6.1 0.2 - - - -
115A VAL* 3.8 25.9 - - + +
194A CYS 3.8 1.6 - - - +
196A ALA* 3.1 39.3 + - + +
198A HIS* 5.0 10.3 - - + +
200A THR* 5.4 0.9 - - - +
201A SER* 3.3 34.5 - - - +
203A SER 4.0 2.5 - - - +
204A PRO* 1.3 69.6 - - - +
206A VAL* 1.3 63.8 + - - +
27M LEU* 4.7 8.1 - - + -
67M SER* 3.2 35.2 - - - +
68M GLY* 4.9 0.7 - - - +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A VAL* 5.1 2.0 - - - -
193A THR* 4.5 12.8 - - + -
194A CYS 3.7 11.4 - - - +
195A GLU* 4.2 13.0 - - + +
204A PRO* 3.3 24.0 + - + +
205A ILE* 1.3 81.4 - - - +
207A LYS* 1.3 80.2 + - - +
208A SER* 4.6 4.5 - - - -
65M SER* 4.3 12.3 - - - -
66M GLY* 3.0 26.9 - - - +
67M SER* 2.8 35.9 + - - +
70M ASP 4.3 1.2 - - - +
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A VAL* 2.8 54.1 + - + +
116A SER* 4.0 4.5 - - - +
117A ILE* 4.0 20.9 - - + +
194A CYS* 3.3 23.4 + - + -
206A VAL* 1.3 87.7 - - - +
208A SER* 1.3 68.4 + - - +
67M SER 3.5 17.5 - - - -
68M GLY* 5.0 3.1 - - - -
69M THR 5.1 1.6 - - - +
70M ASP* 3.6 38.4 + - + +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE* 4.2 10.6 - - - +
191A SER* 4.9 0.9 + - - -
192A TYR 3.5 9.6 + - - -
193A THR* 3.3 25.8 - - - +
206A VAL* 4.6 4.3 - - - -
207A LYS* 1.3 83.6 - - - +
209A PHE* 1.3 75.7 + - - +
210A ASN* 5.4 0.2 + - - -
72M THR* 5.5 5.6 - - - -
74M ARG* 3.3 21.3 + - - -
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Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE* 4.6 15.0 - - + -
118A PHE 5.8 0.2 - - - -
119A PRO* 3.5 35.7 - - + -
132A VAL* 4.5 14.6 - - + -
186A TYR* 3.8 20.0 - + - -
190A ASN 3.0 8.8 - - - +
191A SER* 3.7 0.9 - - - -
192A TYR* 3.0 60.4 + + + -
208A SER* 1.3 81.6 + - - +
210A ASN* 1.3 72.8 + - - +
211A ARG* 4.9 8.7 - - + -
214A CYS 5.6 6.3 - - - -
128B VAL* 6.4 1.8 - - + -
214B ARG* 5.9 0.4 - - - -
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Residues in contact with ASN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASN* 2.9 25.2 - - - +
191A SER* 4.1 8.7 - - - -
208A SER* 5.5 0.2 - - - -
209A PHE* 1.3 86.4 - - - +
211A ARG* 1.3 65.3 + - - +
213A GLU* 3.0 47.2 + - + +
214A CYS 4.0 4.3 + - - +
20M SER* 4.1 9.1 + - - -
74M ARG* 2.6 35.3 + - - +
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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