Contacts of the strand formed by residues 97 - 108 (chain A) in PDB entry 2G1Y
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 3.6 19.5 - - - +
92A ILE 3.8 0.7 - - - +
93A THR* 3.7 2.1 - - - +
94A VAL* 2.8 36.1 + - + +
96A GLY* 1.3 76.4 - - - +
98A THR* 1.3 63.2 + - - +
99A VAL* 3.4 25.6 - - + -
142A ILE* 3.5 32.1 - - + -
145A GLN* 4.0 13.2 - - - +
147A VAL* 4.9 9.9 - - + -
148A LEU* 3.8 20.6 - - + -
173A LEU* 4.2 14.6 - - + -
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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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91A ILE* 4.5 25.4 - - + -
92A ILE 3.6 9.9 - - - +
93A THR* 4.6 13.1 + - - +
96A GLY 3.7 7.1 + - - -
97A ILE* 1.3 75.2 + - - +
99A VAL* 1.3 64.7 - - - +
145A GLN* 3.0 19.3 + - - +
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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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91A ILE* 4.4 3.6 - - - -
92A ILE* 2.7 46.5 + - + +
94A VAL* 5.0 2.0 - - + -
97A ILE* 3.4 19.5 - - + -
98A THR* 1.3 77.6 - - - +
100A THR* 1.3 62.9 + - - +
101A GLN* 3.5 8.5 + - + +
138A ILE* 3.8 32.5 - - + -
141A ASN* 4.8 6.1 - - + +
142A ILE* 3.6 18.6 - - + +
145A GLN* 2.9 26.5 - - - +
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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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89A GLN* 3.6 35.9 - - + +
90A ASP 3.7 9.6 - - - +
91A ILE* 4.1 16.1 - - + +
99A VAL* 1.3 74.7 - - - +
101A GLN* 1.3 64.3 + - - +
141A ASN* 3.7 17.7 - - - +
145A GLN* 5.1 0.2 + - - -
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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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39A VAL* 4.3 9.1 - - + +
89A GLN* 3.3 7.7 - - - +
90A ASP 2.9 31.2 + - - +
92A ILE* 3.6 31.4 - - + -
99A VAL* 3.5 7.3 + - + +
100A THR* 1.3 75.2 + - - +
102A MET* 1.3 77.6 + - - +
103A PHE* 3.7 4.7 - - - -
135A VAL* 4.7 0.2 - - - +
136A THR 2.8 21.7 - - - +
137A PRO* 4.2 0.3 - - - +
138A ILE* 3.1 40.1 + - + +
141A ASN* 2.9 28.2 + - - +
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Residues in contact with MET 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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39A VAL* 4.6 4.5 + - - +
70A ASN* 3.8 25.4 - - - +
87A LEU* 3.5 43.5 - - + -
88A SER 3.3 21.3 - - - +
89A GLN* 4.0 25.1 - - - +
101A GLN* 1.3 90.9 - - - +
103A PHE* 1.3 59.2 + - - +
135A VAL* 3.4 30.5 - - + +
136A THR* 5.3 1.6 - - - +
141A ASN* 5.1 1.4 + - - -
985A NAG 3.9 13.9 - - - +
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Residues in contact with PHE 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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21A ILE* 3.9 15.9 - - + -
39A VAL* 3.5 29.2 - - + +
41A VAL* 4.0 20.4 - - + -
59A PHE* 3.7 26.9 - + - -
67A TYR* 5.8 0.2 - + - -
87A LEU* 3.3 9.5 - - - -
88A SER* 2.7 55.8 + - - +
90A ASP* 3.8 25.8 - - + -
92A ILE* 4.4 13.0 - - + -
101A GLN 3.7 9.6 - - - -
102A MET* 1.3 74.8 - - - +
104A GLY* 1.3 71.6 + - - +
105A GLU* 3.8 21.5 - - + -
135A VAL* 5.6 0.2 - - - -
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Residues in contact with GLY 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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39A VAL 2.8 16.8 + - - -
40A TRP* 3.2 9.6 - - - +
41A VAL 3.1 27.2 + - - +
74A LEU* 4.4 11.2 - - - +
86A PHE 3.4 7.4 - - - -
87A LEU* 4.1 9.1 - - - +
103A PHE* 1.3 79.4 - - - +
105A GLU* 1.3 61.5 + - - -
106A VAL* 3.7 2.5 - - - -
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Residues in contact with GLU 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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41A VAL 3.7 4.5 - - - +
43A SER* 3.1 28.4 + - - -
44A SER* 4.8 1.4 + - - -
45A LYS* 4.9 2.8 - - - +
59A PHE* 3.5 36.0 - - + +
61A ALA* 4.3 8.4 + - - +
67A TYR* 4.1 5.7 + - - -
85A GLY* 3.2 3.7 - - - -
86A PHE* 2.8 59.1 + - + +
88A SER* 2.7 25.9 + - - +
103A PHE* 3.8 19.7 + - + -
104A GLY* 1.3 70.1 - - - -
106A VAL* 1.3 62.5 + - - +
107A THR 3.6 0.3 + - - -
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Residues in contact with VAL 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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40A TRP* 3.3 44.0 - - + -
41A VAL 3.1 8.9 + - - +
42A PRO* 4.0 2.9 - - + +
43A SER* 3.0 27.6 + - - -
46A CYS* 3.6 6.6 - - - +
74A LEU* 6.6 0.2 - - + -
76A LEU* 5.3 2.0 - - + -
83A VAL* 3.8 21.8 - - + -
84A SER 3.2 16.8 - - - +
85A GLY* 4.0 0.9 - - - +
104A GLY* 4.5 1.6 - - - +
105A GLU* 1.3 71.6 - - - +
107A THR* 1.3 61.9 + - - +
108A GLU 3.4 25.6 - - - +
109A MET* 4.2 12.3 - - + +
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Residues in contact with THR 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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43A SER* 4.3 0.9 - - - +
45A LYS* 3.8 28.3 - - + +
46A CYS* 3.6 17.7 - - - -
47A SER* 4.2 1.6 + - - -
50A TYR* 3.3 15.6 - - - -
84A SER 2.7 8.1 + - - -
85A GLY* 3.8 6.6 - - - -
86A PHE* 3.6 33.4 - - + -
105A GLU 3.6 0.4 + - - -
106A VAL* 1.3 76.0 - - - +
108A GLU* 1.3 81.1 + - - +
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Residues in contact with GLU 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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50A TYR* 3.1 31.2 + - + +
83A VAL* 3.3 11.1 - - - -
84A SER* 2.9 52.2 + - - -
85A GLY 4.5 0.2 + - - -
106A VAL* 3.4 4.6 - - - +
107A THR* 1.3 96.9 + - - +
109A MET* 1.3 59.8 + - - +
110A PRO* 3.5 5.6 - - + +
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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