Contacts of the strand formed by residues 89 - 101 (chain A) in PDB entry 1J71
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLN* 4.9 6.1 + - - -
82A ILE* 3.1 16.2 - - - -
83A GLU* 4.1 12.6 - - - -
84A TYR* 4.9 1.6 - - - -
87A LEU 4.8 2.0 + - - -
88A THR* 1.3 77.1 - - - +
90A SER* 1.3 64.4 + - - +
91A GLN* 3.7 17.9 + - - -
117A THR* 3.0 6.1 + - - -
118A SER* 2.9 35.1 + - - -
119A VAL* 4.1 3.1 - - - +
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Residues in contact with SER 90 (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 TRP* 3.1 20.7 - - - -
80A PHE* 4.2 2.7 - - - -
81A SER* 3.4 2.3 - - - -
82A ILE* 3.0 43.2 + - - +
89A SER* 1.3 71.1 + - - +
91A GLN* 1.3 72.3 + - - +
114A VAL* 3.8 22.2 - - - -
116A THR 3.4 6.3 - - - -
117A THR* 2.7 21.8 + - - -
119A VAL* 3.6 3.1 - - - +
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Residues in contact with GLN 91 (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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48A GLN* 4.1 7.3 + - - -
80A PHE 3.3 6.1 - - - +
81A SER* 3.7 21.3 + - - +
82A ILE 4.2 1.4 + - - -
89A SER* 3.7 16.6 + - - -
90A SER* 1.3 98.4 + - - +
92A GLY* 1.3 60.3 + - - +
114A VAL* 3.4 5.1 - - - +
115A THR* 3.0 23.5 + - - -
116A THR* 2.9 38.5 + - - +
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Residues in contact with GLY 92 (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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79A ASP* 3.6 9.0 - - - +
80A PHE* 2.8 34.2 + - - +
91A GLN* 1.3 75.6 - - - +
93A SER* 1.3 61.8 + - - -
113A ASP 3.3 14.6 - - - -
114A VAL* 4.0 3.8 - - - -
115A THR* 4.1 8.7 - - - -
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Residues in contact with SER 93 (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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75A ASN* 4.7 10.2 + - - -
77A ASN* 5.7 1.1 - - - -
78A GLN 3.3 14.6 - - - -
79A ASP* 4.9 5.2 - - - -
80A PHE* 4.2 1.7 - - - +
92A GLY* 1.3 74.6 - - - -
94A PHE* 1.3 65.4 + - - +
95A TYR* 3.4 23.4 + - - -
112A ALA* 4.3 3.1 - - - -
113A ASP* 2.9 30.6 + - - +
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Residues in contact with PHE 94 (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 ASP* 4.2 2.2 - - - -
38A LEU 5.3 0.9 - - - -
75A ASN* 4.0 3.6 - - - +
76A LEU* 3.0 33.4 + - + +
77A ASN 4.1 0.9 + - - -
78A GLN* 2.8 35.4 + - + +
79A ASP 3.9 9.4 - - - -
80A PHE* 3.4 37.7 - + + -
93A SER* 1.3 74.7 - - - +
95A TYR* 1.3 63.7 + - - +
110A GLN* 3.4 29.4 - - + +
111A PHE* 3.5 19.3 - - - -
112A ALA* 3.9 7.4 - - + -
136A ASN* 3.5 29.6 - - + -
138A TYR* 3.8 28.7 - + - -
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Residues in contact with TYR 95 (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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65A PHE* 5.1 2.0 - + - -
67A PRO* 3.7 30.5 - - + +
73A ALA* 4.3 12.1 - - + -
74A GLN 3.1 28.3 - - - -
75A ASN* 3.2 32.8 + - + -
76A LEU* 4.1 2.7 - - - -
93A SER* 3.4 32.0 + - - -
94A PHE* 1.3 76.0 - - - +
96A LYS* 1.3 63.2 + - - +
97A ASP* 5.5 0.2 - - + -
109A GLN 4.4 0.2 - - - -
110A GLN* 3.2 8.7 - - - +
111A PHE* 2.8 51.3 + + + +
113A ASP* 3.7 24.8 + - + -
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Residues in contact with LYS 96 (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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72A SER 3.5 3.5 - - - +
74A GLN* 2.9 58.8 + - + +
76A LEU* 3.7 31.4 - - + -
95A TYR* 1.3 77.8 - - - +
97A ASP* 1.3 63.4 + - - +
108A ASN* 3.5 33.4 + - + +
109A GLN 3.3 3.8 - - - -
110A GLN* 4.2 18.6 - - - +
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Residues in contact with ASP 97 (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 VAL* 4.5 0.4 - - + -
21A GLY* 3.4 16.3 - - - -
65A PHE* 3.8 5.0 - - - -
70A SER* 2.6 26.4 + - - -
72A SER* 2.7 28.0 + - - -
73A ALA* 3.3 19.2 - - + +
95A TYR* 5.5 0.2 - - + -
96A LYS* 1.3 75.4 - - - +
98A THR* 1.3 80.0 + - - +
99A VAL* 3.6 2.8 + - - +
106A ILE 4.1 0.2 - - - +
108A ASN* 4.0 8.0 - - - +
109A GLN* 2.9 33.3 + - - +
111A PHE* 3.5 21.7 - - + -
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Residues in contact with THR 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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19A VAL 3.9 0.4 - - - +
20A VAL* 3.4 5.2 - - - +
21A GLY 2.9 39.3 + - - +
22A SER* 5.6 0.8 - - - -
24A GLN* 5.6 5.8 - - - +
72A SER* 4.2 8.5 + - - -
97A ASP* 1.3 86.8 + - - +
99A VAL* 1.3 64.4 + - - +
100A GLY 5.1 0.2 - - - +
105A SER* 4.1 16.2 - - - +
106A ILE 3.4 13.2 - - - +
107A LYS* 3.9 27.4 - - + +
108A ASN 4.8 0.7 + - - -
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Residues in contact with VAL 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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18A ILE* 4.5 13.2 - - + -
19A VAL 3.4 7.2 - - - +
20A VAL* 4.5 9.2 - - + -
38A LEU* 4.3 20.9 - - + -
97A ASP 4.0 3.1 - - - +
98A THR* 1.3 78.3 - - - +
100A GLY* 1.3 61.4 + - - +
101A PHE* 4.3 21.4 - - + -
105A SER* 3.3 3.1 - - - -
106A ILE* 2.8 47.8 + - + +
109A GLN* 3.9 23.1 - - + -
111A PHE* 4.2 16.2 - - + -
124A MET* 4.9 1.3 - - + -
141A VAL* 5.5 0.7 - - + -
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Residues in contact with GLY 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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18A ILE* 3.3 4.2 - - - +
19A VAL* 2.8 50.0 + - - +
98A THR* 4.3 0.8 - - - +
99A VAL* 1.3 75.8 - - - +
101A PHE* 1.3 68.5 + - - +
104A ILE 3.2 13.5 - - - -
105A SER* 3.9 6.1 - - - -
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Residues in contact with PHE 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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3A VAL* 4.3 8.1 - - + -
5A THR* 3.7 21.8 - - + -
17A ASP 3.9 10.3 - - - +
18A ILE* 3.9 16.6 - - + -
99A VAL* 4.3 15.0 - - + -
100A GLY* 1.3 79.4 - - - +
102A GLY* 1.3 66.7 + - - +
103A GLY 3.0 5.0 + - - +
104A ILE* 3.0 28.4 + - + +
106A ILE* 4.8 7.4 - - + -
124A MET* 4.0 20.9 - - + -
141A VAL* 3.9 30.7 - - + -
145A LEU* 4.0 19.7 - - + -
172A PHE* 3.6 30.1 - + - -
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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