Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 1RP1
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A THR* 3.6 23.0 - - - -
43A ASN* 3.2 7.0 + - - +
68A LYS* 4.3 4.5 - - - +
69A LYS* 3.0 35.2 - - + +
70A THR 4.1 0.9 - - - +
71A ARG* 4.1 16.2 - - + +
93A MET* 4.0 22.7 - - + -
94A PHE* 3.8 14.3 - - + -
97A GLU* 3.4 32.5 - - + +
98A GLU* 1.3 74.0 - - - +
100A ASN* 1.3 75.4 + - - +
101A CYS* 3.7 0.6 + - + -
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Residues in contact with ASN 100 (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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40A LEU* 3.8 14.4 - - + -
41A TYR 3.9 3.8 - - - -
42A THR* 3.9 8.6 - - - +
63A ASN 4.2 0.2 - - - +
64A PHE* 3.5 22.3 - - + -
65A GLN* 2.9 49.0 + - - +
68A LYS* 4.0 4.8 + - - +
69A LYS 3.0 14.1 + - - -
70A THR* 3.2 27.3 + - + +
71A ARG 2.9 26.7 + - - +
99A VAL* 1.3 74.3 - - - +
101A CYS* 1.3 61.0 + - - +
102A ILE 3.9 0.7 - - - -
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Residues in contact with CYS 101 (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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39A LEU 3.5 2.1 - - - +
40A LEU* 3.6 0.8 - - - +
41A TYR* 2.8 46.0 + - - +
71A ARG* 3.4 6.7 - - - +
73A ILE* 3.5 17.0 - - - -
90A CYS* 2.0 57.4 - - + -
93A MET* 3.7 15.0 - - - -
94A PHE* 4.1 10.5 - - + -
99A VAL* 3.7 2.0 + - + -
100A ASN* 1.3 72.5 - - - +
102A ILE* 1.3 60.7 + - - +
103A CYS* 3.9 0.6 + - - -
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Residues in contact with ILE 102 (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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38A PHE* 4.0 29.2 - - + -
39A LEU 3.2 9.6 - - - +
40A LEU* 3.8 16.6 - - + -
52A LEU* 3.9 20.0 - - + -
64A PHE* 4.3 10.1 - - + -
70A THR* 3.6 19.7 - - + -
71A ARG 3.0 7.1 + - - -
72A PHE* 3.1 46.0 - - + +
73A ILE* 2.8 30.4 + - - -
101A CYS* 1.3 75.7 - - - +
103A CYS* 1.3 61.9 + - - +
104A VAL* 3.7 0.7 + - - +
131A MET* 5.2 2.7 - - + -
135A LEU* 5.4 1.1 - - + -
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Residues in contact with CYS 103 (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 ARG 3.4 2.8 - - - +
38A PHE* 3.6 1.2 - - - -
39A LEU* 2.7 52.4 + - + +
41A TYR* 3.9 16.6 - - + -
73A ILE* 3.5 7.6 - - - +
86A LEU* 3.7 36.1 - - + -
87A LEU* 4.1 2.2 - - - -
90A CYS* 3.6 28.0 - - - -
102A ILE* 1.3 72.3 - - - +
104A VAL* 1.3 62.0 + - - +
105A ASP* 3.7 1.6 + - + +
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Residues in contact with VAL 104 (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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36A THR* 3.9 25.1 - - + -
37A ARG 3.4 4.5 - - - +
38A PHE* 3.9 15.9 - - + -
72A PHE* 3.8 29.4 - - + -
73A ILE 2.8 18.0 + - - +
74A ILE* 4.0 20.9 - - + -
75A HIS* 3.2 21.1 + - - -
86A LEU* 4.3 3.0 - - - +
102A ILE* 4.2 1.8 - - + +
103A CYS* 1.3 73.4 - - - +
105A ASP* 1.3 59.5 + - - +
106A TRP* 3.8 5.2 - - + -
124A VAL* 4.1 17.3 - - + -
128A VAL* 4.3 9.9 - - + -
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Residues in contact with ASP 105 (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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35A GLY 3.9 3.5 - - - +
36A THR* 3.5 2.1 - - - -
37A ARG* 2.7 71.2 + - + +
39A LEU* 4.7 13.4 - - + +
75A HIS* 3.5 9.7 - - + +
86A LEU* 6.1 1.1 - - + -
103A CYS* 3.7 2.8 + - + +
104A VAL* 1.3 73.4 - - - +
106A TRP* 1.3 62.3 + - - +
107A LYS* 3.0 26.8 + - - +
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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