Contacts of the strand formed by residues 138 - 145 (chain B) in PDB entry 1S9C
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 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B GLY* 4.3 16.6 - - - -
64B ILE* 4.5 6.1 - - - -
94B LEU* 4.0 3.1 - - + -
95B GLU 3.3 12.1 - - - +
96B LEU* 3.8 18.2 - - + -
97B TYR* 4.1 4.7 - - - -
100B LEU* 4.6 8.3 - - - -
128B VAL 4.0 0.2 - - - +
129B TYR* 3.6 2.4 - - - -
130B SER* 3.0 49.4 + - - -
136B LEU* 3.7 4.7 - - - +
137B ILE* 1.3 84.6 - - + +
139B HIS* 1.3 62.1 + - - +
140B ASN* 4.2 14.1 - - - -
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Residues in contact with HIS 139 (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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93B TYR* 3.7 24.8 - + - +
94B LEU* 3.4 6.3 - - - +
95B GLU* 3.0 30.6 + - + +
97B TYR* 3.6 29.7 + - + +
127B ASP* 2.4 34.0 + - - -
128B VAL 3.5 7.6 - - - -
129B TYR* 3.8 31.7 + + + +
138B CYS* 1.3 75.7 - - - +
140B ASN* 1.3 88.6 + - - +
141B GLN* 4.5 3.1 - - + -
162B LYS* 4.6 12.7 - - - -
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Residues in contact with ASN 140 (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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61B GLY 3.0 21.6 + - - -
62B VAL* 3.5 12.1 - - - -
65B GLY* 3.8 14.5 - - - +
92B GLN* 3.1 19.3 + - - +
93B TYR 3.2 3.0 - - - +
94B LEU* 3.5 21.7 - - - +
127B ASP* 3.3 1.2 - - - -
128B VAL* 2.8 42.9 + - + +
130B SER* 4.8 0.6 + - - -
138B CYS* 4.2 8.9 - - - -
139B HIS* 1.3 80.0 - - - +
141B GLN* 1.3 61.0 + - - +
142B PHE* 3.4 24.0 - - + -
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Residues in contact with GLN 141 (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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91B GLU 4.6 0.2 - - - -
92B GLN* 3.8 3.7 + - - +
93B TYR* 2.9 44.6 + - + +
125B ILE* 3.2 38.0 - - + +
126B MET 3.7 3.4 - - - +
127B ASP* 3.0 27.3 + - - +
139B HIS* 4.2 4.3 - - - +
140B ASN* 1.3 71.7 - - - +
142B PHE* 1.3 64.0 + - - +
143B SER* 3.6 4.9 + - - -
160B LYS 2.9 25.3 + - - -
161B VAL* 4.1 0.9 - - - +
162B LYS* 3.2 38.7 + - - +
243B LYS* 5.1 4.7 + - - -
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Residues in contact with PHE 142 (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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62B VAL* 4.0 10.8 - - + -
65B GLY 3.5 21.5 - - - -
66B GLN* 3.7 24.2 - - + -
68B SER* 5.1 7.0 - - - -
89B HIS* 4.1 14.1 - + - +
91B GLU 4.1 0.4 - - - -
92B GLN* 3.1 30.5 - - - -
124B ILE 3.5 0.9 - - - +
125B ILE* 3.5 0.9 - - - -
126B MET* 3.0 44.1 + - + +
128B VAL* 3.4 21.8 - - + -
140B ASN* 3.4 24.2 - - + -
141B GLN* 1.3 72.5 - - - +
143B SER* 1.3 60.4 + - - +
144B LEU* 3.4 25.2 + - + +
217B LEU* 4.8 1.3 - - + -
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Residues in contact with SER 143 (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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89B HIS* 3.9 1.9 - - - -
90B GLY* 2.9 27.4 + - - -
91B GLU* 3.1 48.2 + - - +
123B VAL* 3.8 18.0 - - - +
124B ILE 3.8 4.0 - - - -
125B ILE* 4.3 16.4 - - - +
141B GLN* 3.6 4.1 + - - -
142B PHE* 1.3 72.0 - - - +
144B LEU* 1.3 59.0 + - - +
243B LYS* 5.3 1.1 - - - -
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Residues in contact with LEU 144 (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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68B SER* 5.9 3.1 - - - +
84B PHE* 5.6 9.0 - - + -
87B VAL* 3.8 23.3 - - + -
88B LEU 3.5 4.7 - - - +
89B HIS* 5.2 9.6 - - + -
90B GLY 4.6 0.2 - - - +
123B VAL* 3.5 4.8 - - - +
124B ILE* 2.9 67.5 + - + +
126B MET* 4.6 21.8 - - + -
142B PHE* 4.3 22.0 - - + +
143B SER* 1.3 75.8 - - - +
145B PHE* 1.3 60.2 + - - +
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Residues in contact with PHE 145 (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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86B LYS 4.8 4.3 - - - -
87B VAL* 3.1 16.6 - - - +
88B LEU* 2.5 79.5 + - + +
90B GLY* 4.9 7.9 - - - +
122B VAL* 2.8 47.6 - - - -
123B VAL* 3.4 17.7 - - + +
124B ILE* 6.3 1.3 - - - -
143B SER 3.9 0.2 + - - -
144B LEU* 1.3 75.3 - - - +
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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