Contacts of the strand formed by residues 91 - 100 (chain B) in PDB entry 6S1M
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 CYS 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B GLY* 3.4 16.4 - - - +
80B LYS* 4.7 6.7 - - + +
85B LEU* 3.6 37.9 - - + -
86B GLN 6.0 1.1 - - - -
89B GLU* 3.4 25.8 - - - +
90B LYS* 1.3 75.2 - - - +
92B CYS* 1.3 61.7 + - - +
93B VAL* 4.9 3.7 - - - +
161B VAL 3.9 0.2 - - - +
162B PHE* 3.2 12.7 - - - -
163B GLY 2.9 42.0 + - - +
164B SER* 4.8 2.5 - - - -
165B VAL* 5.5 1.1 - - - -
171B PHE* 4.9 4.3 - - - -
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Residues in contact with CYS 92 (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 ALA* 4.1 6.7 - - + -
73B TRP* 3.8 23.6 - - + -
78B GLY* 3.0 9.9 + - - +
79B VAL* 3.3 29.0 - - + +
80B LYS* 3.1 27.0 + - - +
91B CYS* 1.3 75.6 - - - +
93B VAL* 1.3 68.5 + - - +
94B VAL* 4.5 2.3 + - - +
160B ALA* 4.1 16.2 - - - -
161B VAL 3.1 12.3 - - - +
162B PHE* 4.5 9.4 - - + -
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Residues in contact with VAL 93 (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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80B LYS 4.1 15.0 - - - +
82B LEU* 4.1 24.9 - - + +
85B LEU* 4.5 10.3 - - + -
91B CYS* 4.9 3.6 - - - +
92B CYS* 1.3 80.6 - - - +
94B VAL* 1.3 69.0 + - - +
95B GLY 4.1 1.0 + - - -
135B LEU* 3.9 17.5 - - + -
137B ASP* 5.9 1.3 - - - +
159B LEU 3.9 0.7 - - - +
160B ALA* 3.3 2.1 - - - -
161B VAL* 2.9 43.9 + - + +
171B PHE* 3.7 36.3 - - + -
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Residues in contact with VAL 94 (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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58B LEU* 4.9 6.3 - - + +
62B ARG* 4.4 28.4 + - + +
65B LEU* 4.0 30.7 - - + -
66B GLU* 4.7 17.5 - - + +
69B ALA* 6.1 0.2 - - + -
79B VAL* 5.2 5.2 - - + -
80B LYS 5.0 1.4 + - - -
92B CYS* 4.7 7.6 - - - +
93B VAL* 1.3 83.2 - - - +
95B GLY* 1.3 60.8 + - - +
137B ASP* 3.8 15.8 - - - +
158B VAL* 4.8 5.2 - - + -
159B LEU 3.5 8.5 - - - +
160B ALA* 3.9 16.4 - - + -
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Residues in contact with GLY 95 (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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58B LEU* 4.3 6.5 - - - -
93B VAL 4.1 1.2 + - - -
94B VAL* 1.3 74.7 - - - +
96B THR* 1.3 62.4 - - - -
135B LEU* 3.7 20.6 - - - +
136B GLU 3.8 8.1 - - - -
137B ASP* 5.1 2.7 - - - -
157B THR 4.1 0.2 - - - +
158B VAL* 3.4 9.2 - - - +
159B LEU* 3.0 32.9 + - - +
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Residues in contact with THR 96 (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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1065A LEU* 5.5 3.4 - - + -
1066A HIS* 3.9 16.2 - - + +
54B TYR* 4.9 13.6 + - + -
57B ARG* 6.2 3.1 - - - +
58B LEU* 3.4 29.5 - - - +
95B GLY* 1.3 71.2 - - - -
97B LEU* 1.3 75.6 + - - +
134B VAL 3.6 0.3 - - - +
135B LEU* 3.7 4.1 - - - +
136B GLU* 2.9 40.7 + - + +
156B GLY* 4.5 15.5 - - - +
157B THR 3.7 8.7 - - - +
158B VAL* 4.5 4.2 - - + +
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Residues in contact with LEU 97 (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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1065A LEU* 4.8 3.8 - - - +
96B THR* 1.3 86.7 - - - +
98B PHE* 1.3 62.7 + - - +
133B LEU* 3.7 42.2 - - + -
134B VAL 3.6 15.9 - - - +
135B LEU* 4.6 2.2 - - + +
136B GLU* 5.6 0.2 - - - +
144B LEU* 4.5 12.3 - - + -
148B ILE* 6.1 3.6 - - + -
153B LEU* 3.8 35.4 - - + -
154B VAL 3.9 18.4 - - - +
155B THR* 4.0 1.9 + - - -
156B GLY 3.6 11.4 + - - -
157B THR* 3.0 20.5 + - - +
159B LEU* 4.3 17.2 - - + +
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Residues in contact with PHE 98 (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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1060A ARG* 4.4 27.1 - - + -
1065A LEU* 4.0 25.1 - - + -
96B THR 5.1 0.4 - - - +
97B LEU* 1.3 76.0 - - - +
99B LYS* 1.3 74.5 + - - +
100B ALA* 3.8 19.3 + - + -
133B LEU* 3.7 3.2 - - - -
134B VAL* 2.9 49.5 + - + +
136B GLU* 4.5 17.7 - - + +
141B ARG* 5.2 7.0 - - - -
155B THR* 3.9 17.0 - - + -
380B ASP* 4.8 10.1 - - - -
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Residues in contact with LYS 99 (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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98B PHE* 1.3 86.2 - - - +
100B ALA* 1.3 61.5 + - - +
101B MET* 3.3 38.4 + - + +
104B GLN* 5.3 1.4 - - - +
127B ILE* 4.5 5.9 - - - +
131B ASP* 3.3 28.0 + - + +
132B GLU 3.5 11.2 - - - +
133B LEU* 3.8 14.4 - - + -
150B VAL 3.3 22.6 + - - -
151B SER* 3.7 15.8 + - - +
153B LEU 3.3 25.1 + - - +
154B VAL* 4.6 3.1 - - - -
155B THR* 3.6 28.4 - - + +
355B TYR* 4.1 8.5 + - + +
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Residues in contact with ALA 100 (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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98B PHE* 3.8 22.1 + - + +
99B LYS* 1.3 70.2 - - - +
101B MET* 1.3 58.6 + - - +
102B PRO* 3.5 10.0 - - - +
131B ASP* 3.8 2.9 - - - +
132B GLU* 2.9 43.0 + - + +
134B VAL* 5.2 6.5 - - + -
143B LYS* 6.0 0.9 - - - +
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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