Contacts of the strand formed by residues 124 - 132 (chain B) in PDB entry 3BRW
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 GLN 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B ASP 4.2 0.3 - - - +
121B ILE* 3.1 26.4 + - - +
123B ASP* 1.3 78.2 - - - +
125B GLU* 1.3 68.5 + - - +
126B HIS* 3.3 9.7 + - + +
143B PRO* 3.3 34.6 - - + +
145B SER* 4.4 13.7 + - - -
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Residues in contact with GLU 125 (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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118B TYR* 2.6 33.2 + - + +
119B ASP 4.1 5.6 - - - -
120B VAL* 3.8 19.0 - - + +
123B ASP 3.5 8.1 + - - +
124B GLN* 1.3 73.0 + - - +
126B HIS* 1.3 60.4 + - - +
143B PRO* 3.6 7.2 - - - +
144B ILE 3.0 32.0 + - - +
145B SER* 3.2 10.2 - - - -
146B CYS* 3.1 38.3 + - - -
150B PHE* 5.6 1.0 - - - -
176C LYS* 4.8 7.3 - - - +
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Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 6.1 0.2 - - - +
118B TYR* 3.8 9.4 - - - -
119B ASP* 3.1 71.6 + - + +
121B ILE* 4.1 18.6 - - + +
124B GLN* 3.3 10.3 + - + +
125B GLU* 1.3 75.7 - - - +
127B LEU* 1.3 70.4 + - - +
128B ARG* 4.1 30.1 + - + +
141B VAL* 4.2 14.1 - - + +
142B ILE 4.2 0.2 - - - -
143B PRO* 3.7 19.5 - - + -
144B ILE* 4.7 2.3 - - - +
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Residues in contact with LEU 127 (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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116B LEU* 4.8 6.3 - - + -
117B LYS 3.4 21.1 - - - +
118B TYR* 4.2 13.0 - - + -
126B HIS* 1.3 81.2 - - - +
128B ARG* 1.3 59.5 + - - +
129B LEU* 3.7 21.7 + - + +
140B ASP 3.9 0.5 - - - +
141B VAL* 3.7 10.4 - - - -
142B ILE* 3.3 26.3 + - + +
144B ILE* 4.4 20.9 - - + -
150B PHE* 4.4 13.7 - - + -
151B PRO* 4.8 7.6 - - + -
156B MET* 3.7 37.9 - - + -
159B LEU* 4.9 7.6 - - + -
175C PRO* 5.8 0.2 - - + -
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Residues in contact with ARG 128 (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 ILE* 4.1 0.8 - - - +
93B HIS* 3.4 56.8 + - - +
94B PHE* 3.4 32.6 - - + -
116B LEU* 3.4 3.1 - - - -
117B LYS* 2.9 47.9 + - + +
119B ASP* 6.0 0.4 + - + -
126B HIS* 4.1 20.4 + - + +
127B LEU* 1.3 70.7 - - - +
129B LEU* 1.3 63.1 + - - +
139B HIS* 3.2 28.9 + - + +
140B ASP 3.6 3.6 - - - -
141B VAL* 3.2 30.9 - - + +
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Residues in contact with LEU 129 (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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94B PHE* 4.6 0.2 - - - -
114B PHE* 3.7 25.1 - - + -
115B SER 3.6 2.9 - - - -
116B LEU* 3.9 15.3 - - + -
127B LEU* 4.0 30.1 - - + +
128B ARG* 1.3 73.7 - - - +
130B LEU* 1.3 62.8 + - - +
131B LEU 4.4 0.2 - - - -
138B TYR 4.5 0.7 - - - -
139B HIS* 3.4 10.7 - - - -
140B ASP* 2.9 32.3 + - + +
142B ILE* 4.1 15.7 - - + -
156B MET* 3.3 28.9 - - + +
159B LEU* 4.1 14.4 - - + -
160B VAL* 4.0 20.0 - - + -
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Residues in contact with LEU 130 (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 THR* 4.6 14.8 - - - +
89B ILE* 4.6 3.6 - - + -
90B TYR* 4.0 17.7 - - + +
94B PHE* 3.8 26.0 - - + -
114B PHE* 3.6 1.6 - - - -
115B SER 2.7 42.9 + - - +
129B LEU* 1.3 76.2 - - - +
131B LEU* 1.3 58.5 + - - +
132B ARG* 3.4 29.3 + - - +
137B THR* 4.2 13.2 - - - +
138B TYR 3.3 16.2 - - - +
139B HIS* 3.9 21.5 - - + -
185B ASP* 4.0 15.5 - - - +
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Residues in contact with LEU 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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112B LEU* 4.6 18.2 - - + -
113B VAL 4.0 0.9 - - - -
114B PHE* 3.7 32.1 - - + -
130B LEU* 1.3 72.3 - - - +
132B ARG* 1.3 65.6 + - - +
133B THR* 3.5 2.1 + - - -
137B THR* 3.3 3.0 - - - -
138B TYR* 2.9 51.3 + - + +
157B ALA* 4.3 13.7 - - + +
160B VAL* 3.8 19.7 - - + +
161B CYS* 3.7 30.1 - - + -
164B VAL* 4.1 12.6 - - + -
169B PHE* 4.4 9.2 - - + -
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Residues in contact with ARG 132 (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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90B TYR* 3.8 4.2 - - - -
111B HIS 3.7 1.0 - - - +
112B LEU* 3.4 12.1 - - - +
113B VAL* 3.0 62.5 + - + +
115B SER* 2.5 37.8 + - - -
130B LEU* 3.4 25.6 + - - +
131B LEU* 1.3 71.8 - - - +
133B THR* 1.3 60.7 + - - +
136B ARG 5.5 0.2 - - - +
137B THR* 3.8 17.5 - - - +
181B ILE* 3.2 21.2 - - - +
184B PHE* 3.6 27.6 - - + -
185B ASP* 2.8 39.9 + - - +
394B LEU* 4.2 11.4 - - + +
397B LEU* 4.9 1.1 - - - -
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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