Contacts of the strand formed by residues 78 - 88 (chain B) in PDB entry 3C9S
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 LEU 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B VAL* 3.7 2.7 - - - -
77B GLY* 1.3 73.7 - - - -
79B PRO* 1.3 71.6 - - + +
80B LYS* 3.9 6.3 - - + +
134B GLY* 3.0 2.3 - - - -
135B GLU* 2.9 36.9 + - + +
192B ILE* 3.6 16.8 - - + -
195B VAL* 3.3 41.3 - - + -
199B GLN* 5.6 1.1 - - - +
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Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.8 40.6 - - + -
72B VAL* 3.9 5.3 - - + -
73B ILE* 4.1 10.3 - - + -
78B LEU* 1.3 91.6 - - + +
80B LYS* 1.3 65.7 + - - +
111B TYR* 3.6 24.9 - - + +
112B LYS 3.7 9.2 - - - +
113B CYS* 3.6 19.8 - - + +
132B LEU* 4.0 12.6 - - + -
133B VAL 4.1 3.8 - - - +
134B GLY* 4.1 3.1 - - - -
192B ILE* 4.7 3.1 - - + -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 4.7 5.3 - - - -
78B LEU* 3.9 12.3 - - + +
79B PRO* 1.3 79.8 - - - +
81B TRP* 1.3 109.3 + - + +
112B LYS 5.1 1.1 - - - +
113B CYS* 3.3 6.8 - - - +
114B GLU* 2.8 22.7 + - - +
132B LEU* 4.4 0.4 - - - +
133B VAL 2.7 18.8 + - - +
134B GLY* 4.1 6.7 - - - -
135B GLU* 3.5 35.8 + - + +
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Residues in contact with TRP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.8 42.4 - - + +
32A GLU 4.0 12.3 - - - -
33A TYR* 3.5 33.0 - + - -
38A LEU* 4.1 15.9 - - + -
40A LEU* 3.4 23.6 - - + -
38B LEU* 5.2 3.4 - - + -
80B LYS* 1.3 115.3 + - + +
82B ALA* 1.3 61.2 + - - +
114B GLU* 3.2 14.1 + - + +
116B VAL* 4.2 14.4 - - + -
132B LEU* 3.3 4.4 - - - +
133B VAL* 2.8 65.5 + - + +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 5.5 0.2 - - - -
65B ILE* 4.4 13.5 - - + -
81B TRP* 1.3 76.2 - - - +
83B LEU* 1.3 67.7 + - - +
113B CYS* 5.6 2.9 - - - -
114B GLU 2.7 13.7 + - - +
115B VAL* 3.2 19.6 - - + -
116B VAL* 2.9 29.0 + - - +
130B VAL* 4.7 4.3 - - + -
131B PHE* 3.1 13.0 - - - +
132B LEU* 3.8 13.5 - - + -
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 4.8 0.2 - - + -
40A LEU* 3.8 17.7 - - + +
41A THR* 3.4 42.2 - - - +
42A THR* 4.2 10.5 - - + -
131A PHE* 4.6 0.9 - - + -
82B ALA* 1.3 77.0 - - - +
84B ILE* 1.3 65.1 + - - +
85B SER 4.2 0.4 - - - -
116B VAL* 3.8 11.7 - - + -
117B GLY* 3.1 42.8 - - - +
118B GLY* 3.8 4.7 - - - +
129B SER 3.9 0.7 - - - +
130B VAL* 3.5 2.4 - - - +
131B PHE* 2.9 58.0 + - + +
900B ACP 5.1 0.7 - - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA* 5.6 2.5 - - + -
65B ILE* 4.2 7.6 - - + -
83B LEU* 1.3 79.9 - - - +
85B SER* 1.3 59.6 + - - +
86B LEU* 3.7 29.6 - - + -
100B PHE* 4.3 5.6 - - + -
101B TYR* 3.9 17.7 - - + +
104B VAL* 3.9 38.6 - - + -
115B VAL* 4.0 15.0 - - + -
117B GLY 3.1 9.0 + - - +
118B GLY* 3.1 6.4 - - - -
119B ASN 3.1 16.3 + - - -
128B ILE* 4.1 12.8 - - + -
129B SER 3.5 7.9 - - - +
130B VAL* 4.6 13.0 - - + -
900B ACP 3.4 11.6 + - - -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 4.2 13.7 - - - -
44A VAL* 3.2 27.6 - - - +
129A SER* 4.0 5.8 + - - -
131A PHE* 4.2 7.5 - - - -
83B LEU 4.2 0.6 - - - -
84B ILE* 1.3 71.4 - - - +
86B LEU* 1.3 60.7 + - - +
87B ASN* 4.2 4.9 + - - -
119B ASN* 3.5 18.1 + - - +
127B GLY 3.7 2.1 - - - +
128B ILE* 3.9 0.9 - - - -
129B SER* 2.8 47.8 + - - -
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.9 0.7 - - + -
84B ILE* 3.7 22.9 - - + -
85B SER* 1.3 74.7 + - - +
87B ASN* 1.3 58.3 + - - +
88B LEU* 3.8 29.8 + - + +
97B VAL* 5.0 3.8 - - + -
100B PHE* 4.1 12.6 - - + -
101B TYR* 3.6 33.2 - - + +
119B ASN 2.7 13.2 + - - +
120B ILE* 3.4 9.7 - - + -
121B SER* 2.8 32.2 + - - +
126B ILE* 5.5 0.2 - - + -
127B GLY 3.4 2.0 - - - +
128B ILE* 3.7 29.8 - - + -
900B ACP 3.7 8.7 - - - +
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.4 7.5 - - - +
46A ASN* 4.0 19.1 - - - +
87A ASN* 4.1 18.7 + - - -
129A SER* 5.1 5.4 + - - -
85B SER* 4.6 7.8 + - - -
86B LEU* 1.3 72.4 - - - +
88B LEU* 1.3 62.2 + - - +
121B SER* 3.2 28.7 + - - -
123B SER* 3.1 23.7 + - - +
125B LYS 4.4 0.4 - - - +
126B ILE* 3.3 4.7 - - - -
127B GLY* 2.8 46.1 + - - +
129B SER* 5.7 1.3 + - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.7 28.5 - - + -
11A LEU* 4.0 8.5 - - + -
86B LEU* 3.8 27.4 - - + +
87B ASN* 1.3 82.0 - - - +
89B PRO* 1.3 67.6 - - + +
90B GLU* 3.5 1.0 + - - -
92B LEU* 4.0 19.1 - - + -
96B TYR* 5.9 1.8 - - + -
97B VAL* 4.3 9.0 - - + -
120B ILE* 3.8 32.3 - - + -
121B SER 2.6 11.9 + - - +
122B LYS* 3.3 10.0 - - - -
123B SER* 3.0 19.0 + - - -
126B ILE* 4.2 14.8 - - + -
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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