Contacts of the strand formed by residues 126 - 133 (chain B) in PDB entry 3SJ5
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 ALA 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PRO* 3.7 1.6 - - - +
122B VAL* 2.9 26.8 + - + -
123B ALA* 3.3 11.0 + - + +
124B LYS 3.7 0.2 - - - -
125B ASP* 1.3 88.0 - - - +
127B ILE* 1.3 68.3 + - - +
175B ARG* 3.8 35.2 - - + +
176B ILE 3.1 14.1 - - - +
177B LYS* 4.1 3.8 - - + -
178B PHE* 4.3 2.0 - - - -
182B VAL* 3.9 3.1 - - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 3.8 25.4 - - + -
95B LEU* 4.1 36.6 - - + -
96B MET* 4.5 8.7 - - + -
119B ALA* 4.3 16.6 - - + -
120B LYS 3.3 12.8 - - - +
121B PRO* 4.0 14.1 - - + -
122B VAL* 3.9 5.2 - - - -
126B ALA* 1.3 80.7 - - - +
128B GLU* 1.3 61.8 + - - +
129B MET* 5.1 0.9 - - + -
175B ARG* 3.4 5.2 - - - +
176B ILE* 2.8 48.5 + - + +
178B PHE* 3.9 15.5 - - + -
182B VAL* 4.8 4.5 - - + -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ILE 3.8 0.7 - - - +
119B ALA* 3.1 6.4 - - - +
120B LYS* 2.5 62.1 + - - +
122B VAL* 3.7 23.2 - - + +
127B ILE* 1.3 74.3 - - - +
129B MET* 1.3 62.2 + - - +
130B GLU* 6.0 0.6 - - + +
161B VAL* 5.5 5.4 - - + +
173B LYS* 3.2 46.3 + - + +
174B VAL 3.3 9.2 - - - +
175B ARG* 4.4 5.6 - - + +
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.4 39.9 - - + +
98B MET* 4.0 11.7 - - + -
117B LEU* 3.6 29.2 - - + +
118B ILE 3.4 3.6 - - - +
119B ALA* 4.2 7.2 - - + -
127B ILE* 4.3 1.5 + - + -
128B GLU* 1.3 75.3 - - - +
130B GLU* 1.3 62.4 + - - +
131B TYR 4.1 0.6 + - - -
141B PHE* 4.2 11.8 - - + -
145B ILE* 4.5 3.8 - - - -
172B LEU 3.8 1.0 - - - +
173B LYS* 3.4 2.5 - - - -
174B VAL* 2.8 44.8 + - + +
176B ILE* 4.2 19.3 - - + -
502B HEM 4.0 29.2 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 3.2 13.7 - - - +
117B LEU* 3.4 12.2 - - - -
118B ILE* 3.0 18.8 + - + +
128B GLU* 6.0 0.4 - - + -
129B MET* 1.3 74.7 - - - +
131B TYR* 1.3 69.9 + - - +
132B VAL* 3.7 10.4 + - + +
141B PHE* 4.7 1.6 - - - -
162B GLU* 4.7 3.8 - - - +
171B ARG* 3.2 44.1 + - - +
172B LEU 3.4 8.9 + - - +
173B LYS* 3.9 34.5 + - + +
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Residues in contact with TYR 131 (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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115B PRO* 3.8 4.7 - - + -
116B ARG 3.5 3.1 - - - -
117B LEU* 4.0 8.7 - - + -
130B GLU* 1.3 72.7 - - - +
132B VAL* 1.3 63.5 + - - +
133B SER* 3.2 28.5 + - - -
136B LYS* 3.4 7.7 + - - -
137B MET 2.9 32.0 + - - -
138B TYR* 4.0 30.1 - + - -
141B PHE* 3.8 42.5 - + + -
170B SER 4.4 3.6 - - - -
171B ARG* 3.1 5.7 - - - -
172B LEU* 2.8 39.3 + - + +
502B HEM 2.6 44.1 + - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PRO 4.6 0.9 - - - +
115B PRO* 3.6 0.5 - - - +
116B ARG* 2.9 48.9 + - + +
130B GLU* 3.8 18.8 - - + +
131B TYR* 1.3 80.8 - - - +
133B SER* 1.3 65.0 + - - +
169B PHE* 4.0 28.4 - - + -
170B SER 3.4 3.4 - - - -
171B ARG* 3.8 39.9 - - + +
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Residues in contact with SER 133 (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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113B THR 5.0 1.7 + - - -
114B PRO 5.4 0.9 - - - -
115B PRO* 4.1 6.1 - - - +
131B TYR* 3.2 27.4 + - - -
132B VAL* 1.3 78.5 - - - +
134B LYS* 1.3 66.1 + - - +
135B ARG* 3.1 12.1 + - - +
136B LYS 3.8 0.3 + - - -
169B PHE* 4.3 6.7 - - - -
170B SER* 2.9 36.0 + - - -
502B HEM 2.6 25.7 + - - -
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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
------------------------------------------------------------
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