Contacts of the strand formed by residues 94 - 107 (chain A) in PDB entry 1S8B
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLY* 4.3 7.6 - - - -
69A LEU 4.4 4.7 - - - +
89A TRP* 4.7 2.0 - - - -
93A MET* 1.3 108.2 - - + +
95A ILE* 1.3 67.1 + - - +
96A ILE* 4.2 13.6 - - - +
97A SER* 4.3 13.7 + - - -
131A MET* 2.9 61.4 - - + +
132A ILE 4.6 0.2 - - - +
133A LEU 4.5 2.2 - - - -
134A SER* 3.2 36.5 + - - -
136A MET* 6.3 3.1 - - + -
154A PHE* 4.9 1.8 - - + -
157A ALA* 5.1 7.4 - - + +
159A THR* 5.5 4.2 - - + +
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Residues in contact with ILE 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 ALA* 4.0 19.5 - - + -
67A GLY 5.5 0.2 - - - +
68A GLY* 3.4 6.5 - - - -
69A LEU* 2.9 26.5 + - - +
85A TRP* 5.6 6.7 - - + +
86A TYR 5.6 0.4 - - - -
87A PRO* 4.6 9.0 - - + -
89A TRP* 3.1 49.0 - - + +
94A TYR* 1.3 72.5 - - - +
96A ILE* 1.3 78.9 + - + +
117A MET* 3.7 11.0 - - + -
131A MET 2.8 8.5 + - - -
132A ILE* 2.6 48.5 - - + +
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Residues in contact with ILE 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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47A ARG* 5.7 6.3 - - - +
69A LEU* 3.6 16.4 - - + +
71A MET* 6.1 0.7 - - + -
85A TRP* 5.5 15.5 - - + -
94A TYR* 4.2 2.8 - - - +
95A ILE* 1.3 102.0 - - + +
97A SER* 1.3 67.8 + - - +
106A LYS* 5.6 14.8 - - - +
132A ILE* 2.9 18.3 + - + +
133A LEU* 3.3 22.6 - - + +
134A SER 3.0 23.2 + - - -
146A PHE* 6.3 3.8 - - + -
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Residues in contact with SER 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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69A LEU 3.0 6.3 + - - +
70A LEU* 3.1 35.4 - - - +
71A MET* 2.8 35.3 + - - +
93A MET* 6.1 1.0 - - - +
94A TYR* 4.3 19.2 + - - -
95A ILE 4.2 0.2 - - - -
96A ILE* 1.3 80.5 - - - +
98A GLY* 1.3 55.1 + - - +
99A SER* 4.2 2.5 - - - -
134A SER* 3.2 12.6 - - - -
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Residues in contact with GLY 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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47A ARG* 5.1 3.8 - - - -
71A MET* 3.1 11.7 - - - -
96A ILE* 4.3 1.0 - - - +
97A SER* 1.3 71.7 - - - +
99A SER* 1.3 60.7 + - - -
101A LEU* 5.4 3.8 - - - -
133A LEU* 5.4 1.6 - - - +
134A SER 3.0 7.3 + - - +
135A ILE* 3.2 3.1 - - - +
136A MET 2.9 14.6 + - - -
138A ILE* 2.9 31.5 - - - +
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Residues in contact with SER 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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70A LEU* 5.6 1.6 - - - -
71A MET 3.0 7.1 + - - -
72A ILE* 3.3 37.5 - - - +
73A PRO 3.5 0.5 - - - -
97A SER* 4.2 3.3 - - - -
98A GLY* 1.3 74.8 - - - +
100A LEU* 1.3 98.0 + - - +
101A LEU* 3.2 7.0 + - - +
136A MET* 3.0 25.7 + - - +
138A ILE* 4.3 0.9 - - - -
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Residues in contact with LEU 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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72A ILE* 5.4 1.3 - - + -
73A PRO* 3.2 29.8 - - + +
74A ALA 3.8 0.9 + - - +
99A SER* 1.3 102.9 + - - +
101A LEU* 1.3 57.6 + - - +
136A MET* 3.0 12.0 + - + -
137A ASP* 3.3 34.1 + - + +
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Residues in contact with LEU 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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47A ARG* 3.8 20.2 - - - +
71A MET 5.1 3.6 - - - +
74A ALA* 3.0 43.1 - - + +
75A GLY 4.1 0.2 - - - +
76A ILE 5.0 0.2 - - - +
77A TYR* 5.1 2.9 - - + +
98A GLY* 5.6 2.0 - - - -
99A SER 3.6 9.9 - - - +
100A LEU* 1.3 79.3 - - - +
102A ALA* 1.3 91.3 + - - +
103A ALA 4.4 1.1 - - - +
104A THR* 2.5 40.4 - - + +
137A ASP 3.4 4.3 + - - +
138A ILE* 3.2 21.2 - - + +
139A LEU* 3.0 22.9 + - - +
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Residues in contact with ALA 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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12A PHE* 5.4 0.7 - - + -
74A ALA 3.2 5.1 + - - +
75A GLY* 3.2 4.4 - - - -
76A ILE 2.9 22.5 + - - -
101A LEU* 1.3 84.9 - - - +
103A ALA* 1.3 64.9 + - + +
139A LEU* 3.2 11.7 - - + +
140A ASN* 3.3 15.3 - - - +
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Residues in contact with ALA 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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11A THR* 4.3 0.9 - - - -
12A PHE* 4.0 14.4 - - + +
13A PRO* 3.8 17.7 - - + -
18A LYS* 3.0 8.7 + - - -
76A ILE* 3.6 26.2 - - + +
77A TYR 2.9 24.6 + - - -
102A ALA* 1.3 71.0 - - + +
104A THR* 1.3 57.7 + - - +
139A LEU 3.1 0.8 + - - -
140A ASN* 2.3 30.0 + - - +
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Residues in contact with THR 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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11A THR* 2.6 25.4 - - - +
47A ARG* 6.0 0.2 - - - +
77A TYR 3.2 9.2 + - - +
79A PRO* 4.3 12.1 - - + -
101A LEU* 2.5 48.4 - - + +
103A ALA* 1.3 72.8 + - - +
105A GLU* 1.3 61.9 + - - +
106A LYS* 4.7 1.6 - - + +
138A ILE* 4.4 4.7 - - + -
140A ASN 3.0 6.1 + - - -
141A ILE* 2.6 49.0 - - + +
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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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11A THR* 3.4 21.6 + - + -
13A PRO 4.8 0.5 - - - +
14A ALA* 4.6 0.9 - - - -
15A GLU* 3.4 33.9 + - - +
18A LYS* 4.7 1.3 + - - +
77A TYR 3.4 4.6 + - - -
78A ALA* 3.2 10.1 - - + +
79A PRO* 2.7 36.6 - - - +
104A THR* 1.3 79.0 - - - +
106A LYS* 1.3 56.2 + - - +
107A ASN* 2.9 36.5 + - + +
142A LYS* 3.3 25.4 - - + +
144A SER* 5.1 4.6 + - - +
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Residues in contact with LYS 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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58A MET* 4.1 8.2 - - - +
79A PRO* 3.2 33.7 - - + +
81A CYS* 2.8 47.9 - - - +
96A ILE* 5.6 16.2 - - - -
104A THR* 4.7 1.9 - - + +
105A GLU* 1.3 72.2 - - - +
107A ASN* 1.3 62.1 - - - +
133A LEU* 5.4 14.6 - - + -
141A ILE* 5.3 3.6 - - + -
142A LYS 3.0 6.6 + - - +
143A ILE* 3.2 22.2 - - + -
144A SER 3.1 22.9 + - - -
146A PHE* 4.6 11.3 - - + +
156A ARG* 5.7 2.7 - - - +
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Residues in contact with ASN 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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15A GLU* 2.8 26.7 + - - +
79A PRO 3.1 3.4 + - - -
80A ILE* 2.8 28.6 - - - +
81A CYS* 2.8 39.3 + - - -
105A GLU* 2.9 32.1 + - + +
106A LYS* 1.3 76.9 - - - +
108A SER* 1.3 66.8 + - - +
109A ARG* 4.9 0.5 - - - -
144A SER* 3.1 25.1 - - - +
145A HIS* 4.9 2.2 - - + +
146A PHE* 5.3 0.7 - - - -
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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