Contacts of the strand formed by residues 97 - 111 (chain A) in PDB entry 1R5C
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 TYR 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A SER 4.4 8.1 - - - +
26A CYS* 3.6 19.9 - - + +
27A ASN* 2.7 30.9 + - - +
30A MET* 3.8 43.1 - - + +
36A THR* 3.9 6.6 - - + +
40A CYS* 3.5 10.6 - - - +
41A LYS 2.7 42.4 + - - -
42A PRO 4.2 2.2 - - - -
84A CYS* 4.1 4.0 - - + -
85A ARG 3.4 12.6 - - - +
86A GLU* 3.6 28.5 - - + -
87A THR* 4.1 6.4 - - - +
95A CYS* 3.6 23.8 - - + -
96A ALA* 1.3 76.2 - - - +
98A LYS* 1.3 62.3 + - - +
99A THR* 3.9 1.9 + - - -
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Residues in contact with LYS 98 (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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26A CYS* 4.4 0.4 - - - -
83A ASP* 3.3 6.9 - - - +
84A CYS* 3.5 2.6 - - - -
85A ARG* 2.7 39.1 + - + +
87A THR* 4.0 13.2 - - + +
97A TYR* 1.3 72.8 - - - +
99A THR* 1.3 80.0 + - - +
100A THR* 3.6 15.9 + - - +
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Residues in contact with THR 99 (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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22A SER 4.1 14.8 - - - +
23A SER* 3.5 24.1 + - - +
25A TYR* 4.1 7.8 + - + -
26A CYS* 3.1 33.7 + - - +
82A THR* 3.9 19.7 - - + -
97A TYR 3.9 1.0 + - - -
98A LYS* 1.3 87.2 - - - +
100A THR* 1.3 65.0 + - - +
101A GLN* 4.7 16.6 + - + +
19B PRO* 5.3 0.9 - - + -
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Residues in contact with THR 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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82A THR* 3.3 2.1 - - - -
83A ASP* 2.7 57.2 + - + +
98A LYS* 3.6 17.2 + - - +
99A THR* 1.3 78.3 + - - +
101A GLN* 1.3 65.7 + - - +
102A VAL* 3.8 23.3 + - + +
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Residues in contact with GLN 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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22A SER* 5.5 4.9 + - - -
48A HIS* 5.7 0.6 - - + -
80A ARG* 4.6 14.0 + - - +
81A ILE 3.5 6.1 - - - +
82A THR* 3.7 17.7 - - - +
99A THR* 4.7 12.2 - - + +
100A THR* 1.3 76.8 - - - +
102A VAL* 1.3 67.0 + - - +
19B PRO* 3.3 36.1 - - + +
20B SER* 4.3 17.0 + - - +
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Residues in contact with VAL 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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80A ARG* 3.7 3.1 - - - +
81A ILE* 3.0 50.0 + - + +
83A ASP* 5.2 7.9 - - + -
100A THR* 3.8 22.4 - - + +
101A GLN* 1.3 80.3 - - - +
103A GLU* 1.3 65.5 + - - +
104A LYS* 3.8 25.1 - - + -
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Residues in contact with GLU 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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78A THR* 4.1 24.2 + - - +
79A MET 3.3 7.0 - - - +
80A ARG* 4.0 32.8 + - + +
102A VAL* 1.3 78.6 - - - +
104A LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 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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78A THR* 3.9 7.2 - - - -
79A MET* 2.8 32.6 + - - +
81A ILE* 4.1 3.9 - - + +
102A VAL* 3.8 27.5 - - + -
103A GLU* 1.3 80.1 - - - +
105A HIS* 1.3 64.7 + - - +
106A ILE* 3.8 3.4 + - - +
123A SER* 3.2 37.3 + - - +
124A VAL* 3.7 26.8 - - - +
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Residues in contact with HIS 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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74A GLN* 4.2 14.3 + - + -
75A SER* 3.0 31.6 - - - +
76A LYS 3.4 16.6 + - - -
77A SER* 3.4 21.9 - - - -
78A THR* 3.4 19.0 + - + +
104A LYS* 1.3 74.6 - - - +
106A ILE* 1.3 58.8 + - - +
123A SER* 3.0 7.6 - - - -
124A VAL* 2.7 60.3 + - + +
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Residues in contact with ILE 106 (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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47A VAL* 4.5 7.2 - - + -
54A VAL* 4.2 17.5 - - + -
57A VAL* 4.4 8.2 - - + +
73A TYR 3.8 0.5 - - - +
74A GLN* 3.3 4.2 - - - +
75A SER* 2.7 46.4 + - - +
79A MET* 3.8 23.3 - - + -
81A ILE* 3.8 27.1 - - + -
104A LYS 4.3 4.5 - - - +
105A HIS* 1.3 79.4 - - - +
107A ILE* 1.3 61.8 + - - +
108A VAL* 3.8 22.0 - - + -
120A PHE* 3.6 28.9 - - + -
122A ALA 3.5 3.6 - - - -
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A VAL* 3.8 23.3 - - + -
64A THR 5.3 1.1 - - - +
72A CYS* 4.0 9.9 - - + -
73A TYR 3.2 9.6 - - - +
74A GLN* 4.0 19.3 - - + +
106A ILE* 1.3 78.5 - - - +
108A VAL* 1.3 62.9 + - - +
120A PHE* 3.7 2.3 - - - -
121A ASP* 2.7 47.6 + - + +
122A ALA* 2.7 37.8 + - + +
124A VAL* 4.2 21.8 - - + -
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Residues in contact with VAL 108 (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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54A VAL* 5.1 1.1 - - + +
57A VAL* 4.0 21.3 - - + -
72A CYS* 3.3 7.2 - - - -
73A TYR* 2.9 27.1 + - + +
106A ILE* 3.8 24.0 - - + -
107A ILE* 1.3 81.5 - - - +
109A ALA* 1.3 61.7 + - - +
110A CYS* 3.9 21.8 + - - -
117A PRO* 4.2 15.7 - - + -
119A HIS 3.2 15.0 - - - +
120A PHE* 4.2 6.5 - - + -
121A ASP* 4.1 1.1 - - - +
8B PHE* 4.2 19.1 - - + -
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Residues in contact with ALA 109 (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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71A ASN* 3.3 8.7 - - - +
72A CYS* 3.7 7.5 - - - -
108A VAL* 1.3 73.5 - - - +
110A CYS* 1.3 59.8 + - - +
117A PRO* 3.4 3.8 - - - +
118A VAL* 2.8 25.8 + - + -
119A HIS* 2.9 23.8 + - + +
125A CPA 3.0 44.4 - - + +
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Residues in contact with CYS 110 (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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58A CYS* 2.0 56.3 - - + -
71A ASN* 3.0 30.2 + - - +
73A TYR* 3.7 21.3 - - + -
108A VAL* 3.9 13.5 - - - -
109A ALA* 1.3 78.9 - - - +
111A GLY* 1.3 57.5 + - - +
115A SER* 3.7 14.3 + - - +
116A VAL 3.1 5.2 - - - +
117A PRO* 4.3 0.2 - - - -
118A VAL* 4.1 3.4 - - - -
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Residues in contact with GLY 111 (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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71A ASN* 5.0 1.8 - - - -
110A CYS* 1.3 75.6 - - - +
112A GLY* 1.3 64.6 + - - -
114A PRO 3.6 1.0 - - - +
115A SER* 4.0 3.5 + - - -
116A VAL* 2.9 36.0 + - - +
118A VAL* 3.9 17.5 - - - +
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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