Contacts of the strand formed by residues 71 - 83 (chain A) 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 VAL 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A HIS* 4.6 1.0 - - - +
66A ALA* 3.0 28.4 + - + +
67A LYS* 3.3 9.2 + - - +
69A LEU 3.9 2.9 - - - +
70A GLY* 1.3 82.6 - - - +
72A VAL* 1.3 70.7 + - - +
73A LEU* 3.7 0.8 + - + -
93A SER* 3.3 27.1 - - - +
94A MSE 3.4 12.3 - - - +
95A GLY* 5.0 1.8 - - - -
97A ASN 5.5 0.9 - - - +
100A ASN* 3.8 11.9 - - + -
101A ALA* 3.7 24.5 - - + +
104A LEU* 3.5 32.1 - - + -
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Residues in contact with VAL 72 (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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21A GLU* 3.6 17.3 - - - +
25A LYS* 3.9 17.7 - - + +
27A PHE* 3.6 27.1 - - + -
63A HIS* 4.8 8.1 - - + -
70A GLY 4.2 0.6 + - - -
71A VAL* 1.3 71.7 - - - +
73A LEU* 1.3 60.3 + - - +
74A LYS* 3.7 23.3 + - + -
92A VAL 3.5 1.7 - - - +
93A SER* 3.4 3.3 - - - -
94A MSE 2.9 52.7 + - + +
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Residues in contact with LEU 73 (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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59A PHE* 3.4 16.6 - - + -
62A TRP* 4.0 30.7 - - + +
63A HIS* 2.8 33.0 + - - -
66A ALA* 3.7 19.3 - - + +
71A VAL* 3.7 4.4 + - + -
72A VAL* 1.3 75.0 - - - +
74A LYS* 1.3 66.5 + - - +
91A CYS* 5.2 1.8 - - + -
92A VAL 3.2 17.5 - - - +
93A SER* 4.0 15.9 - - - +
104A LEU* 5.3 6.3 - - + +
105A TYR* 5.5 1.8 - - + -
108A PHE* 3.9 46.7 - - + -
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Residues in contact with LYS 74 (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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0A ALA 3.9 22.6 + - - +
1A VAL* 3.4 30.7 - - + +
18A TYR* 4.0 23.8 - - + +
21A GLU* 2.8 38.2 + - - +
25A LYS* 4.9 2.1 - - - +
59A PHE* 3.7 4.0 - - - -
63A HIS* 4.7 2.9 - - + -
72A VAL* 3.7 15.5 - - + -
73A LEU* 1.3 82.7 - - - +
75A MSE 1.3 63.4 + - - +
91A CYS* 3.3 4.3 - - - +
92A VAL* 2.9 41.6 + - + +
94A MSE 4.7 0.7 - - + -
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Residues in contact with MSE 75 (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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1A VAL 3.1 4.1 + - - +
2A LEU* 3.5 27.1 - - + -
3A LYS* 2.9 22.2 + - - +
18A TYR* 4.0 9.1 + - - -
55A LEU* 4.8 8.1 - - + -
58A TRP* 4.8 2.2 - - - -
59A PHE* 3.5 37.2 - - + -
74A LYS* 1.3 78.7 - - - +
76A ALA* 1.3 63.7 + - - +
77A HIS* 3.7 28.3 - - + -
89A PHE* 3.8 8.5 - - + -
90A LEU 3.3 11.9 - - - +
91A CYS* 3.9 9.2 - - + +
108A PHE* 3.9 11.7 - - + -
112A PHE* 3.6 28.9 - - + -
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Residues in contact with ALA 76 (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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3A LYS* 3.0 23.8 - - + +
5A ILE* 4.9 0.7 - - + -
9A LEU* 4.0 10.8 - - + -
14A LEU* 4.0 27.4 - - + -
18A TYR* 4.4 6.7 - - - +
75A MSE 1.3 77.6 - - - +
77A HIS* 1.3 63.5 + - - +
89A PHE* 3.5 4.3 - - - -
90A LEU* 2.9 33.3 + - + +
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Residues in contact with HIS 77 (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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2A LEU* 5.6 0.2 - - + -
3A LYS 2.9 7.4 + - - +
4A ILE* 3.5 7.5 - - + +
5A ILE 3.0 23.2 + - - -
9A LEU* 3.8 5.6 - - - -
48A PHE* 3.7 24.0 - + - -
50A ILE* 4.2 9.5 - - + +
55A LEU* 5.4 2.5 - - + -
75A MSE 3.7 12.3 - - + +
76A ALA* 1.3 74.7 - - - +
78A SER* 1.3 87.8 + - - +
88A SER 3.4 11.7 - - - -
89A PHE* 3.7 15.0 - + + -
112A PHE* 3.5 26.5 - + - -
118A ILE* 3.6 19.6 - - + +
74D GLY 3.0 31.7 + - - -
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Residues in contact with SER 78 (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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5A ILE 3.2 5.8 - - - -
7A GLY 2.6 25.1 + - - -
8A ALA* 3.6 0.3 - - - -
9A LEU* 3.6 7.2 + - - +
48A PHE* 3.7 7.7 - - - +
50A ILE* 3.6 7.9 - - - +
77A HIS* 1.3 92.0 + - - +
79A LEU* 1.3 58.1 + - - +
82A VAL* 3.4 22.4 - - - +
87A SER 3.4 21.5 + - - -
88A SER* 2.8 17.7 + - - -
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Residues in contact with LEU 79 (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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4A ILE* 4.1 14.8 - - + -
5A ILE 2.6 15.9 + - - +
6A GLN* 3.1 23.6 + - - +
7A GLY* 2.9 24.1 + - - -
48A PHE 3.5 17.5 - - - +
49A ASP* 4.1 2.2 - - - +
50A ILE* 3.6 34.8 - - + +
52A GLU* 3.8 20.9 - - - +
78A SER* 1.3 73.9 - - - +
80A GLY* 1.3 63.1 + - - +
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Residues in contact with GLY 80 (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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6A GLN* 4.0 9.0 - - - -
47A SER* 3.1 14.2 - - - -
48A PHE* 2.9 43.1 + - - +
79A LEU* 1.3 77.1 - - - +
81A ASP* 1.3 63.4 + - - -
82A VAL* 3.7 1.2 + - - +
128A ARG* 4.5 3.1 - - - -
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Residues in contact with ASP 81 (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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6A GLN* 4.7 3.6 - - - +
7A GLY* 3.3 19.1 - - - -
8A ALA 4.0 0.7 + - - -
46A LEU 3.4 3.8 - - - -
47A SER* 2.8 23.9 + - - -
79A LEU 3.9 0.8 + - - -
80A GLY* 1.3 71.5 - - - -
82A VAL* 1.3 65.3 + - - +
83A LEU* 4.3 7.0 - - + -
86A GLN* 5.1 0.3 - - - +
123A LEU* 3.7 25.3 - - + +
128A ARG* 4.8 2.1 + - - +
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Residues in contact with VAL 82 (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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7A GLY 4.2 2.9 - - - -
8A ALA* 4.1 4.7 - - + +
37A VAL* 3.8 23.3 - - + +
45A GLY* 3.3 1.2 - - - -
46A LEU 2.7 39.5 + - - +
48A PHE* 4.1 11.0 - - + -
78A SER* 3.4 32.1 - - - +
80A GLY 3.9 7.0 - - - +
81A ASP* 1.3 80.5 - - - +
83A LEU* 1.3 65.5 + - - +
86A GLN* 3.7 25.1 - - + +
87A SER 3.8 16.4 - - - +
88A SER* 4.2 0.2 - - - -
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Residues in contact with LEU 83 (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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37A VAL* 3.7 6.9 - - - +
44A GLN* 3.6 21.3 - - + +
81A ASP* 5.0 5.4 - - + -
82A VAL* 1.3 80.6 - - - +
84A ILE* 1.3 70.8 + - - +
85A GLY 3.3 0.2 + - - -
86A GLN* 2.9 44.1 + - - +
123A LEU* 4.7 12.8 - - + -
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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