Contacts of the strand formed by residues 100 - 115 (chain A) in PDB entry 2ARP
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 ILE 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.8 15.7 - - + -
92A LEU* 3.5 29.8 - - + -
93A TYR 3.8 3.6 - - - -
94A TYR* 3.8 23.1 - - + +
99A ASN* 1.3 69.5 - - - +
101A ILE* 1.3 66.1 + - - +
151F VAL* 3.9 24.7 - - + -
152F VAL 3.7 25.4 - - - +
153F ASP* 4.0 2.2 - - - -
154F GLN 3.4 10.9 + - - -
195F THR* 3.8 20.4 - - + +
196F CYS* 5.0 0.7 - - - -
200F ARG* 4.1 4.0 - - - +
201F SER* 2.7 25.3 + - - +
304F GOL 2.9 20.1 + - - -
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Residues in contact with ILE 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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91A MET 3.8 0.7 - - - +
92A LEU* 3.1 6.9 - - - -
93A TYR* 2.9 61.0 + - + +
95A ASP* 3.6 35.7 - - + +
99A ASN 3.6 7.6 - - - +
100A ILE* 1.3 87.5 - - - +
102A LYS* 1.3 67.5 + - - +
103A LYS* 4.0 12.6 - - + +
154F GLN* 3.5 22.0 - - + +
304F GOL 3.6 24.5 - - - +
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Residues in contact with LYS 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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90A SER* 4.2 8.3 - - - -
91A MET 3.4 12.3 - - - +
92A LEU* 3.6 16.3 - - + +
101A ILE* 1.3 72.3 - - - +
103A LYS* 1.3 70.3 + - - +
104A ASP* 3.0 34.2 + - - +
105F LEU 4.4 1.3 - - - +
106F ASP 2.7 32.6 + - - -
107F GLY* 4.8 0.2 - - - -
153F ASP* 3.7 17.5 - - - +
154F GLN* 3.0 24.7 + - - -
159F TYR* 3.5 27.1 + - + +
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER* 3.3 1.9 - - - -
91A MET 2.8 32.5 + - - +
93A TYR* 3.3 31.2 - - + +
101A ILE* 4.0 13.6 + - + +
102A LYS* 1.3 82.8 + - - +
104A ASP* 1.3 65.0 + - - +
105A ILE* 3.5 26.3 + - + +
401A 1PG 5.7 0.9 - - - -
154F GLN* 4.3 8.7 - - - +
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Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO* 5.2 4.0 - - + -
89A MET 3.9 5.4 - - - -
90A SER* 2.6 28.4 + - - +
102A LYS* 3.0 26.8 + - - +
103A LYS* 1.3 71.3 - - - +
105A ILE* 1.3 64.3 + - - +
106A GLN* 3.8 18.2 + - - +
106F ASP* 4.0 7.3 - - - +
124F GLN* 5.7 1.8 - - - -
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Residues in contact with ILE 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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88A PRO* 3.0 4.2 - - - +
89A MET 2.8 44.7 + - - +
91A MET* 4.6 9.9 - - + -
93A TYR* 4.7 2.2 - - + -
103A LYS* 3.5 38.1 - - + +
104A ASP* 1.3 72.6 - - - +
106A GLN* 1.3 68.3 + - - +
108A MET* 3.3 31.3 - - + +
401A 1PG 4.0 45.1 - - - +
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Residues in contact with GLN 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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88A PRO* 3.7 30.9 - - - +
104A ASP* 4.2 16.4 + - - +
105A ILE* 1.3 87.2 - - - +
107A ASN* 1.3 84.1 + - - +
108A MET* 3.3 1.4 + - - +
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Residues in contact with ASN 107 (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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86A LEU* 3.6 42.8 - - + +
87A ARG 3.7 9.0 + - - -
106A GLN* 1.3 86.1 + - - +
108A MET* 1.3 62.1 + - - +
109A ILE 3.5 2.0 - - - -
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Residues in contact with MET 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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20A PHE* 5.4 0.7 - - + -
35A TYR* 2.9 41.5 + - + +
37A ALA* 4.3 4.2 - - - +
87A ARG 2.9 8.1 + - - +
89A MET* 3.9 31.9 - - + +
91A MET* 3.8 34.5 - - + -
105A ILE* 3.3 48.0 - - + +
106A GLN 3.8 0.9 - - - +
107A ASN* 1.3 77.8 - - - +
109A ILE* 1.3 59.8 + - + +
110A VAL* 4.4 0.8 + - - +
401A 1PG 4.8 11.9 - - - +
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Residues in contact with ILE 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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35A TYR* 3.6 22.7 - - + -
36A HIS 3.7 13.9 - - - +
37A ALA 3.6 4.3 - - - -
38A ASN* 3.9 4.7 - - - +
86A LEU* 3.1 10.0 - - - +
87A ARG* 2.9 33.5 + - + +
88A PRO 3.8 20.0 - - - +
89A MET* 4.1 8.3 - - + -
107A ASN 3.5 0.4 - - - -
108A MET* 1.3 80.0 - - + +
110A VAL* 1.3 75.6 + - - +
111A GLU* 4.5 2.9 - - - +
125F PRO* 4.0 32.3 - - + -
126F GLU* 3.8 29.4 - - + +
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Residues in contact with VAL 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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13A LYS* 3.4 9.2 - - + +
37A ALA 2.8 18.4 + - - +
38A ASN* 2.8 45.1 + - + +
39A TYR* 4.7 5.6 - - - -
40A CYS* 3.9 5.8 - - - -
83A PRO* 3.8 16.4 - - + -
86A LEU* 3.7 20.2 - - + -
108A MET 6.0 0.4 - - - -
109A ILE* 1.3 72.5 - - - +
111A GLU* 1.3 58.4 + - - +
112A GLU 3.8 18.6 - - - +
113A CYS* 3.8 21.1 - - - -
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Residues in contact with GLU 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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2A LEU* 4.5 0.5 - - - +
13A LYS* 3.3 29.4 + - - -
38A ASN* 5.3 0.9 + - - -
85A LYS* 2.9 24.1 + - + +
86A LEU* 4.4 1.8 - - - -
87A ARG* 3.8 43.3 + - + +
109A ILE* 3.5 3.7 + - - +
110A VAL* 1.3 74.1 - - - +
112A GLU* 1.3 63.2 + - + +
503A NI 3.9 18.4 - - - +
75F LYS* 4.4 11.6 + - - -
121F CYS 5.3 3.2 - - - +
125F PRO* 3.7 22.2 - - - +
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Residues in contact with GLU 112 (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 GLY 5.6 0.5 + - - -
2A LEU* 2.5 40.4 - - + +
13A LYS* 4.8 0.2 - - - -
83A PRO* 3.3 7.3 - - - +
84A THR* 2.8 35.7 + - - +
85A LYS* 2.8 57.9 + - + +
110A VAL* 3.8 3.5 - - - +
111A GLU* 1.3 80.2 - - - +
113A CYS* 1.3 58.6 + - - +
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Residues in contact with CYS 113 (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 GLY 5.3 0.9 + - - -
2A LEU* 2.9 35.4 - - + +
11A CYS* 3.9 7.5 - - - +
12A CYS 3.8 5.6 - - - -
13A LYS* 3.5 21.1 - - - -
40A CYS* 2.0 56.1 - - + -
82A VAL 3.3 4.7 - - - -
84A THR* 3.5 6.2 + - - +
110A VAL* 3.8 7.0 - - - -
112A GLU* 1.3 78.0 - - - +
114A GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 114 (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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11A CYS* 3.5 12.9 - - - -
80A CYS 3.3 0.7 - - - +
82A VAL* 2.8 34.9 + - - +
84A THR* 3.3 15.9 - - - +
113A CYS* 1.3 76.8 - - - +
115A CYS* 1.3 65.5 + - - -
116A SER 3.4 0.7 + - - -
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Residues in contact with CYS 115 (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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10A ILE* 6.3 0.7 - - - -
11A CYS* 3.6 17.0 - - - +
43A GLU 4.1 1.6 - - - -
44A CYS* 2.0 56.3 - - + -
45A PRO* 4.9 6.5 - - - +
79A SER* 4.3 5.2 - - - +
80A CYS 3.6 0.2 - - - -
84A THR* 5.7 1.4 - - - +
114A GLY* 1.3 70.5 - - - -
116A SER* 1.3 65.6 + - - +
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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