Contacts of the strand formed by residues 311 - 320 (chain B) in PDB entry 3POS
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 PHE 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B PHE* 3.5 10.0 - + + -
83B PRO* 3.2 22.9 - - - +
84B PHE* 3.0 49.7 + + + +
86B ASN* 3.3 30.7 - - + -
91B LEU* 3.7 19.5 - - + -
112B LEU* 3.9 34.1 - - + -
113B PHE 3.6 2.9 - - - -
129B ASN* 3.4 26.9 - - + -
130B ILE* 3.9 8.7 - - + -
308B TYR* 3.6 27.8 - + + -
310B ASN* 1.3 77.1 - - - +
312B GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 312 (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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80B SER* 3.4 1.0 - - - -
81B PHE* 2.8 45.2 + - - +
83B PRO* 4.6 0.4 - - - -
113B PHE 2.8 12.5 + - - -
115B ASN* 3.4 26.3 - - - +
310B ASN* 3.6 2.2 + - - -
311B PHE* 1.3 74.2 - - - +
313B VAL* 1.4 63.0 + - - +
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Residues in contact with VAL 313 (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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78B SER* 3.5 30.7 - - - +
79B ALA 3.4 13.0 - - - +
80B SER* 4.2 3.8 - - - -
81B PHE* 3.4 7.9 - - - -
111B LYS 3.7 0.5 - - - +
112B LEU* 3.5 3.8 - - - -
113B PHE* 2.8 37.7 + - + +
114B PRO 4.6 7.4 - - - +
115B ASN* 4.4 8.7 - - - +
117B LEU* 3.9 28.0 - - + +
119B GLN* 4.0 23.8 - - + +
312B GLY* 1.4 85.1 - - - +
314B LEU* 1.3 63.7 + - - +
315B GLY 4.5 0.7 - - - +
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Residues in contact with LEU 314 (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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23B PHE* 4.2 13.0 - - + -
37B TRP* 3.9 18.7 - - + -
78B SER* 3.2 1.6 - - - -
79B ALA 2.9 34.8 + - - +
81B PHE* 3.5 12.3 - - + -
93B VAL* 4.7 3.8 - - + -
94B GLN 6.0 0.7 - - - +
110B VAL* 4.1 20.6 - - + -
111B LYS 3.3 5.2 - - - +
112B LEU* 3.9 22.0 - - + -
313B VAL* 1.3 75.4 - - - +
315B GLY* 1.3 65.8 + - - +
316B LEU* 4.8 0.9 - - + -
330B PHE* 3.9 38.6 - - + -
331B LEU 6.1 0.2 - - - +
332B ILE* 4.0 14.8 - - + -
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Residues in contact with GLY 315 (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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77B LEU 3.6 6.5 - - - -
78B SER* 3.7 9.2 - - - -
110B VAL* 3.4 8.1 - - - +
111B LYS* 2.8 39.9 + - - +
113B PHE* 4.2 4.0 - - - -
122B MET* 4.0 12.6 - - - -
313B VAL 4.1 0.6 - - - -
314B LEU* 1.3 76.3 - - - +
316B LEU* 1.3 63.6 + - - -
317B ASP* 3.7 3.0 + - - -
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Residues in contact with LEU 316 (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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37B TRP* 4.1 22.7 - - + -
49B PHE* 3.9 35.1 - - + -
66B LEU* 4.3 11.7 - - + -
75B TYR 3.5 2.1 - - - +
76B ALA* 3.2 6.1 + - - -
77B LEU* 2.7 35.1 + - + +
109B TYR 3.9 15.5 - - - +
110B VAL* 4.0 16.4 - - + -
122B MET* 3.7 0.6 - - - +
314B LEU* 4.8 0.7 - - + -
315B GLY* 1.3 70.8 - - - -
317B ASP* 1.3 58.1 + - - +
318B LEU* 4.0 7.0 - - + -
327B PHE* 3.9 36.8 - - + -
330B PHE* 4.1 15.0 - - + -
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Residues in contact with ASP 317 (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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46B PHE* 5.6 1.6 - - - -
75B TYR 3.3 8.8 - - - +
76B ALA* 4.2 8.3 - - - +
109B TYR* 3.3 22.2 + - - -
111B LYS* 2.7 42.2 + - + +
122B MET* 3.9 16.4 - - + +
123B HIS* 3.6 25.9 - - - -
124B GLY* 3.5 14.1 + - - -
315B GLY 3.7 2.2 + - - -
316B LEU* 1.3 73.6 - - - +
318B LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 318 (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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49B PHE* 5.2 0.7 - - + -
68B THR* 4.6 5.6 - - + -
74B PHE* 3.3 9.2 - - - +
75B TYR* 2.7 56.3 + - + +
107B GLY* 3.8 23.1 - - - +
109B TYR* 3.8 39.7 - - + +
316B LEU* 4.4 8.7 - - + -
317B ASP* 1.3 81.7 - - - +
319B TRP* 1.3 58.7 + - - +
320B GLN* 3.7 30.3 - - + +
327B PHE* 3.9 17.5 - - + -
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Residues in contact with TRP 319 (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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72B ALA* 3.4 35.0 - - + -
73B ARG* 3.3 35.0 - - - -
74B PHE* 3.6 45.5 - + + -
105B CYS* 4.3 16.2 - - - -
106B GLY* 3.2 3.5 - - - -
107B GLY 3.0 24.8 + - - +
109B TYR* 4.8 3.2 + - - -
318B LEU* 1.3 76.7 - - - +
320B GLN* 1.4 70.9 + - - +
321B VAL* 3.5 23.2 - - + +
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Residues in contact with GLN 320 (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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68B THR* 2.7 34.1 + - + +
71B ASP 4.1 0.3 - - - -
72B ALA* 3.1 24.1 + - - -
73B ARG 3.1 12.7 + - - -
75B TYR* 4.4 9.4 - - + -
99B HIS* 4.4 0.2 - - - -
103B ILE* 3.7 12.7 - - - +
105B CYS 3.7 4.7 - - - -
106B GLY* 3.9 3.8 - - - -
107B GLY 3.0 22.2 + - - -
318B LEU* 3.7 14.0 - - + +
319B TRP* 1.4 83.2 - - - +
321B VAL* 1.3 62.2 + - - +
322B LYS 3.8 6.2 - - - +
323B SER* 3.4 13.7 - - - -
325B THR* 2.9 29.5 + - - +
327B PHE* 4.9 0.4 - - - -
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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