Contacts of the strand formed by residues 87 - 95 (chain B) in PDB entry 3RPF
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ALA* 3.7 5.0 - - - +
9B LEU* 2.9 39.4 + - - +
11B THR* 3.0 27.7 + - - -
34B VAL* 3.5 18.0 - - - +
35B GLY 3.4 11.7 - - - -
36B ILE* 4.2 7.7 - - - +
78B SER* 3.4 2.3 + - - -
82B VAL* 3.9 1.2 - - - +
85B GLY 5.3 0.5 + - - -
86B GLN* 1.3 74.7 - - - +
88B SER* 1.3 60.8 + - - +
89B PHE 4.7 2.2 - - - -
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Residues in contact with SER 88 (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 LEU* 4.0 3.4 - - - -
35B GLY 3.1 10.1 + - - -
36B ILE 5.1 0.3 - - - -
37B VAL* 4.1 16.3 + - - +
46B LEU* 5.5 0.2 - - - +
48B PHE* 3.6 30.1 - - - -
77B HIS* 3.3 9.7 + - - -
78B SER* 2.9 35.4 + - - -
82B VAL* 4.2 2.9 - - - -
86B GLN 3.9 0.6 + - - -
87B SER* 1.3 74.3 - - - +
89B PHE* 1.3 59.3 + - - +
74C GLY 3.1 23.1 + - - -
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Residues in contact with PHE 89 (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 LEU* 3.7 3.0 - - - +
33B PHE* 3.7 36.1 - + - -
34B VAL* 3.4 6.4 - - - +
35B GLY* 2.8 28.1 + - - +
75B MSE 3.9 13.7 - - + -
76B ALA 3.5 12.3 - - - -
77B HIS* 3.7 12.8 - + + -
87B SER 3.7 0.6 - - - -
88B SER* 1.3 83.3 + - - +
90B LEU* 1.3 74.9 + - - +
91B CYS* 3.9 23.8 - - + -
108B PHE* 4.3 4.7 - + - -
109B ILE* 5.2 7.9 - - + -
112B PHE* 3.7 36.3 - + + -
113B LYS* 5.4 3.1 - - + -
74C GLY* 3.6 31.9 - - - -
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Residues in contact with LEU 90 (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 LEU* 3.7 15.9 - - + +
11B THR* 3.5 37.0 - - + +
14B LEU* 4.3 10.8 - - + -
15B LEU* 3.7 18.2 - - + -
18B TYR* 3.1 42.0 - - + +
32B VAL* 4.5 0.4 - - + -
33B PHE 3.2 7.9 - - - +
34B VAL* 3.6 14.1 - - + -
75B MSE 3.3 2.8 - - - +
76B ALA* 2.8 34.3 + - + +
89B PHE* 1.3 79.8 - - - +
91B CYS* 1.3 70.2 + - - +
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Residues in contact with CYS 91 (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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32B VAL* 3.4 6.1 - - - +
33B PHE* 2.9 43.8 + - - +
73B LEU* 5.6 2.5 - - + -
74B LYS 3.3 12.3 - - - +
75B MSE 3.9 11.0 - - + +
89B PHE* 3.9 16.8 - - + -
90B LEU* 1.3 81.0 - - - +
92B VAL* 1.3 61.9 + - - +
105B TYR* 4.8 6.6 - - - -
108B PHE* 4.1 15.0 - - + -
109B ILE* 3.9 28.0 - - - -
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Residues in contact with VAL 92 (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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18B TYR* 3.7 31.9 - - + -
30B PHE* 3.6 35.2 - - + -
31B CYS 3.2 11.2 - - - +
32B VAL* 4.4 4.3 - - + -
72B VAL 3.6 0.6 - - - +
73B LEU* 3.4 8.6 - - - +
74B LYS* 2.9 53.2 + - + +
91B CYS* 1.3 76.3 - - - +
93B SER* 1.3 70.6 + - - +
94B MSE 4.2 12.6 - - + -
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Residues in contact with SER 93 (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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31B CYS* 2.8 36.0 + - - +
71B VAL* 3.4 15.9 - - - +
72B VAL 3.5 4.0 - - - -
73B LEU* 4.1 13.0 - - - -
91B CYS* 6.5 0.2 - - - -
92B VAL* 1.3 75.2 - - - +
94B MSE 1.3 60.0 + - - +
101B ALA* 2.7 28.7 + - - -
104B LEU* 4.2 2.1 - - - +
105B TYR* 3.9 24.5 + - - -
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Residues in contact with MSE 94 (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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18B TYR* 3.5 25.6 - - + +
21B GLU* 3.5 31.2 - - + +
22B ALA* 3.7 19.7 - - + -
27B PHE* 3.7 16.5 - - + -
29B ALA 3.3 13.2 - - - +
30B PHE* 4.1 17.9 - - + -
71B VAL* 3.4 3.8 - - - +
72B VAL* 2.8 58.5 + - + +
74B LYS* 4.7 3.8 - - + -
92B VAL* 4.2 16.6 - - + -
93B SER* 1.3 76.8 + - - +
95B GLY* 1.3 59.0 + - - +
101B ALA* 4.2 6.3 - - - -
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Residues in contact with GLY 95 (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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27B PHE* 3.4 20.3 - - - +
28B GLY 3.1 13.3 + - - -
29B ALA* 3.1 14.7 + - - +
70B GLY 4.1 8.1 - - - -
71B VAL* 4.7 4.3 - - - -
94B MSE 1.3 75.6 - - - +
96B LYS* 1.3 68.6 + - - +
97B ASN 3.4 7.4 + - - -
101B ALA* 4.2 6.0 - - - +
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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