Contacts of the strand formed by residues 110 - 121 (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 GLY 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B LEU* 4.4 7.0 - - - -
106B ASP* 2.9 40.5 + - - +
107B THR 4.9 0.2 - - - -
108B ALA 3.5 1.6 - - - -
109B LEU* 1.3 79.6 - - - +
111B HIS* 1.3 69.4 + - - +
112B LEU* 3.7 0.9 + - - +
134B LYS* 5.2 9.2 - - - +
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Residues in contact with HIS 111 (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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104B SER 4.2 3.4 - - - -
105B LEU* 3.9 20.3 - - + +
109B LEU 4.1 0.6 + - - +
110B GLY* 1.3 75.9 - - - -
112B LEU* 1.3 69.7 + - - +
132B ARG 3.7 5.9 - - - +
134B LYS* 4.1 13.0 + - + +
391B ALA 5.7 0.7 - - - -
394B LEU* 3.8 29.4 - - + +
395B GLU* 3.0 41.6 + - + +
398B TYR* 3.1 44.1 - + + -
399B GLU* 5.5 2.9 - - + -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.2 25.1 - - - +
104B SER* 3.1 21.6 + - - +
106B ASP* 3.8 20.6 - - + +
109B LEU* 4.6 18.2 - - + +
110B GLY 3.8 8.1 - - - +
111B HIS* 1.3 86.0 - - - +
113B VAL* 1.3 65.4 + - - +
114B PHE 4.0 0.7 - - - -
131B LEU* 4.6 12.3 - - + -
132B ARG 3.4 11.4 - - - +
133B THR* 4.4 13.5 - - - -
164B VAL* 4.3 20.2 - - + -
166B VAL* 5.3 1.6 - - + -
169B PHE* 4.1 29.2 - - + -
398B TYR* 4.1 1.7 - - - -
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Residues in contact with VAL 113 (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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101B ASN* 5.3 1.8 - - + -
102B TYR 3.5 7.9 - - - +
103B TYR* 4.8 1.6 - - + -
112B LEU* 1.3 77.0 - - - +
114B PHE* 1.3 62.6 + - - +
115B SER* 5.1 0.2 - - - +
130B LEU 3.9 0.2 - - - +
131B LEU* 4.7 0.7 - - - -
132B ARG* 3.0 63.0 + - + +
181B ILE* 4.6 13.2 - - + -
394B LEU* 3.8 19.7 - - + +
397B LEU* 4.1 13.0 - - + -
398B TYR* 4.5 15.9 - - + -
401B LEU* 3.8 28.3 - - + -
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Residues in contact with PHE 114 (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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101B ASN* 3.2 4.7 - - - +
102B TYR* 2.7 44.8 + + + +
112B LEU 4.0 0.6 - - - -
113B VAL* 1.3 73.1 - - - +
115B SER* 1.3 77.3 + - - +
116B LEU* 3.7 19.5 - - + -
129B LEU* 3.7 35.0 - - + -
130B LEU 3.5 10.1 - - - -
131B LEU* 3.7 23.6 - - + -
153B VAL* 3.6 37.9 - - + -
156B MET* 3.8 1.8 - - + -
157B ALA* 3.6 30.7 - - + -
160B VAL* 4.4 1.3 - - + -
169B PHE* 3.8 17.5 - + + -
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Residues in contact with SER 115 (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* 3.5 14.9 - - - -
94B PHE* 4.0 11.2 - - - -
100B PHE 3.3 5.2 - - - -
101B ASN* 3.1 20.1 + - - +
113B VAL* 5.1 0.9 - - - +
114B PHE* 1.3 76.3 + - - +
116B LEU* 1.3 61.4 + - - +
128B ARG 4.0 0.3 - - - +
129B LEU* 3.6 0.9 - - - -
130B LEU* 2.7 38.4 + - - +
132B ARG* 2.5 32.2 + - - -
181B ILE* 4.4 2.8 - - - +
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Residues in contact with LEU 116 (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* 3.6 3.4 - - - -
99B HIS* 3.4 3.6 - - - +
100B PHE* 2.8 64.8 + - + +
102B TYR* 3.8 23.6 - - + +
114B PHE* 3.7 22.2 - - + -
115B SER* 1.3 74.8 - - - +
117B LYS* 1.3 64.8 + - - +
118B TYR 5.3 0.4 - - - +
127B LEU* 4.8 7.4 - - + -
128B ARG 3.4 4.5 - - - -
129B LEU* 3.9 18.2 - - + -
153B VAL* 4.3 0.9 - - + -
156B MET* 3.7 35.0 - - + -
175C PRO* 4.9 8.7 - - + -
408C MET* 6.3 0.2 - - - -
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Residues in contact with LYS 117 (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 HIS* 3.1 37.4 + - + +
94B PHE* 3.5 19.1 - - + -
97B LYS* 3.5 33.2 - - - +
98B GLU 3.4 21.8 - - - +
99B HIS* 4.2 3.8 - - + +
100B PHE* 5.6 0.7 - - - -
116B LEU* 1.3 77.7 - - - +
118B TYR* 1.3 65.6 + - - +
119B ASP* 2.7 32.7 + - + +
127B LEU* 3.4 10.4 - - - +
128B ARG* 2.9 42.3 + - + +
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Residues in contact with TYR 118 (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 GLU* 4.8 4.9 + - - +
100B PHE* 5.8 2.8 - - + -
116B LEU* 5.3 1.2 - - + +
117B LYS* 1.3 79.1 - - - +
119B ASP* 1.3 64.2 + - - +
120B VAL* 3.4 22.3 - - + +
125B GLU* 2.6 39.5 + - + -
126B HIS 3.8 9.9 - - - -
127B LEU* 4.2 8.5 - - + -
144B ILE* 5.6 3.1 - - + -
150B PHE* 3.6 23.6 - + + -
175C PRO* 3.7 34.8 - - + +
176C LYS* 3.7 30.5 - - + -
179C ARG* 3.1 35.8 + - - -
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Residues in contact with ASP 119 (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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117B LYS* 2.7 40.0 + - + +
118B TYR* 1.3 74.5 - - - +
120B VAL* 1.3 74.8 + - - +
121B ILE* 3.8 20.2 - - - +
126B HIS* 3.1 66.0 + - + +
128B ARG* 6.0 0.2 + - - -
179C ARG* 5.9 0.2 - - - +
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Residues in contact with VAL 120 (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* 3.4 37.0 - - + +
119B ASP* 1.3 75.7 + - - +
121B ILE* 1.3 69.6 + - - +
122B GLY 4.0 7.4 + - - +
123B ASP* 3.7 30.3 - - + -
124B GLN 4.4 2.5 - - - -
125B GLU* 3.8 14.6 - - + +
179C ARG* 4.6 13.7 - - - +
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Residues in contact with ILE 121 (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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119B ASP* 3.8 21.9 + - - +
120B VAL* 1.3 76.5 - - - +
122B GLY* 1.3 63.1 + - - +
123B ASP 3.0 8.3 + - - -
124B GLN* 3.1 25.3 + - - +
126B HIS* 4.1 18.6 + - + +
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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