Contacts of the strand formed by residues 15 - 19 (chain B) in PDB entry 3UR9
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 GLY 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LYS* 3.0 18.4 + - - +
12B PHE 2.8 24.5 + - - -
13B GLY 3.2 0.6 + - - -
14B SER* 1.3 82.2 - - - +
16B TRP* 1.3 66.0 + - - -
31B VAL* 3.7 8.0 - - - +
137B GLY 3.6 11.4 - - - -
139B CYS 3.4 12.1 - - - -
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Residues in contact with TRP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 4.0 18.8 - - + -
10B THR* 3.2 10.8 - - - +
11B LYS* 3.3 55.1 - - + +
12B PHE* 3.6 6.7 + - - +
15B GLY* 1.3 78.1 + - - -
17B GLY* 1.3 58.8 + - - +
27B THR* 2.7 26.5 + - - -
31B VAL* 4.1 0.8 - - - +
88B LYS* 3.2 55.0 + - + -
89B ARG 4.0 9.9 - - - -
90B ASP* 3.8 17.2 + - - -
137B GLY 2.9 24.1 + - - -
138B ASP* 4.1 9.4 - - - +
139B CYS 2.9 12.4 + - - +
140B GLY* 3.1 21.5 - - - -
141B ALA* 4.2 4.0 - - + +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.5 8.7 - - - +
10B THR 2.8 30.5 + - - -
16B TRP* 1.3 75.1 - - - +
18B PHE* 1.3 61.6 + - - +
25B PHE* 3.3 23.3 - - - -
26B ILE 3.1 14.1 - - - -
27B THR* 3.9 1.3 - - - -
140B GLY 4.0 6.5 - - - -
142B PRO* 5.6 0.2 - - - -
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Residues in contact with PHE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.8 18.4 - - + -
8B ARG* 3.4 40.4 - - + -
9B VAL* 4.0 8.3 - - + -
17B GLY* 1.3 74.8 - - - +
19B TRP* 1.3 72.9 + - - +
20B VAL* 3.3 11.6 + - + -
25B PHE* 3.4 6.6 - - - -
26B ILE* 2.8 46.9 + - + +
71B MET* 3.6 23.3 - - + -
86B LEU* 4.7 1.8 - - + -
140B GLY 4.8 2.5 - - - +
142B PRO* 3.4 39.5 - - + -
144B VAL* 4.5 2.9 - - + -
153B VAL* 3.9 27.6 - - + -
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Residues in contact with TRP 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A SER 4.6 3.2 + - - -
8B ARG* 2.9 44.2 + - + +
10B THR* 3.3 31.2 + - - +
18B PHE* 1.3 71.7 - - - +
20B VAL* 1.3 60.5 - - - +
21B SER 3.5 17.0 - - - +
22B PRO 4.0 6.7 - - - -
23B THR 4.3 0.4 - - - -
24B VAL 3.5 14.8 - - - -
25B PHE* 3.4 22.5 - + + -
40B PHE* 3.7 28.7 - + - -
60B PHE* 3.7 28.3 - + - -
64B MET* 3.4 33.9 - - + -
65B ARG* 3.7 32.0 - - + +
68B LEU* 3.5 18.8 - - + -
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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