Contacts of the strand formed by residues 124 - 132 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A VAL* 4.1 0.2 - - - -
121A ILE* 3.0 34.4 + - - +
123A ASP* 1.3 79.0 + - - +
125A GLU* 1.3 62.5 + - - +
126A HIS 3.7 0.9 + - - -
247B HIS* 3.5 36.7 + - + +
249B GLN* 3.3 14.1 + - - +
87D GLN* 3.1 34.7 + - - +
91D ASN* 3.2 34.1 + - - +
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 2.7 36.8 + - + -
119A ASP 3.7 6.1 - - - +
120A VAL* 3.7 16.6 - - + +
123A ASP 3.3 13.2 + - - +
124A GLN* 1.3 71.7 - - - +
126A HIS* 1.3 59.6 + - - +
143A PRO* 3.5 5.5 - - - +
144A ILE* 2.8 44.9 + - + +
145A SER 4.0 16.8 - - - +
146A CYS* 5.3 7.5 - - - -
150A PHE* 5.9 0.2 - - - -
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Residues in contact with HIS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 4.1 8.0 - - - -
119A ASP* 2.8 67.9 + - + +
121A ILE* 3.4 41.0 - - + +
125A GLU* 1.3 75.2 - - - +
127A LEU* 1.3 74.9 + - - +
128A ARG* 3.5 39.7 + - + -
141A VAL* 3.4 27.6 - - + +
142A ILE 3.4 8.1 - - - +
143A PRO* 3.9 5.8 - - + -
144A ILE* 4.8 2.0 - - - +
87D GLN* 5.8 2.2 - - - +
125D VAL* 5.0 5.3 - - + +
130D GLN* 5.8 1.1 - - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 5.6 4.7 - - + -
117A LYS 3.4 8.3 - - - +
118A TYR* 4.1 23.1 - - + +
126A HIS* 1.3 78.2 + - - +
128A ARG* 1.3 64.5 + - - +
129A LEU* 3.4 22.4 + - + +
142A ILE* 2.8 43.0 + - + +
144A ILE* 4.9 10.8 - - + -
150A PHE* 3.7 30.7 - - + -
151A PRO* 5.3 8.7 - - + -
156A MET* 3.5 33.9 - - + -
159A LEU* 5.9 0.9 - - + -
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ILE* 4.2 1.3 - - - -
93A HIS* 3.3 51.5 + - - +
94A PHE* 3.6 32.0 - - + -
116A LEU* 3.5 3.8 - - - -
117A LYS* 2.9 44.8 + - + +
119A ASP* 5.2 3.0 + - - -
126A HIS* 3.5 26.4 + - + +
127A LEU* 1.3 70.6 - - - +
129A LEU* 1.3 60.5 + - - +
139A HIS* 3.3 29.5 + - + +
140A ASP 4.1 3.6 - - - -
141A VAL* 3.7 12.2 - - + +
122D ASP 4.9 0.4 + - - -
124D ARG 2.4 32.9 + - - +
125D VAL* 4.4 7.1 - - - +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.0 13.5 - - + -
115A SER 4.0 1.8 - - - -
116A LEU* 3.7 25.4 - - + -
127A LEU* 3.7 27.8 - - + +
128A ARG* 1.3 76.3 - - - +
130A LEU* 1.3 61.1 + - - +
131A LEU 4.3 0.2 - - - -
138A TYR 4.4 1.3 - - - -
139A HIS* 3.1 23.8 - - - -
140A ASP 3.1 19.5 + - - +
142A ILE* 3.4 27.4 - - + -
156A MET* 3.3 35.7 - - + +
160A VAL* 3.8 19.1 - - + -
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A THR* 5.0 5.2 - - - +
89A ILE* 4.0 14.8 - - + -
90A TYR* 3.9 34.3 - - + +
94A PHE* 4.1 15.7 - - + -
114A PHE* 3.3 3.4 - - - -
115A SER* 2.7 39.9 + - - +
129A LEU* 1.3 74.5 - - - +
131A LEU* 1.3 57.2 + - - +
132A ARG* 3.5 29.4 + - - +
137A THR* 4.6 11.9 - - - +
138A TYR 3.4 4.5 - - - +
139A HIS* 3.5 37.9 - - + -
185A ASP* 4.5 2.2 - - - +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 6.3 0.4 - - + -
112A LEU* 3.9 22.7 - - + -
114A PHE* 3.6 26.9 - - + -
130A LEU* 1.3 73.4 - - - +
132A ARG* 1.3 78.2 + - - +
133A THR* 4.1 4.0 + - + +
137A THR* 3.3 2.5 + - - -
138A TYR* 2.6 59.4 + - + +
157A ALA* 4.2 26.9 - - + +
160A VAL* 4.2 8.3 - - + +
161A CYS* 4.3 4.0 - - + -
164A VAL* 3.9 27.1 - - + -
169A PHE* 4.8 1.1 - - + -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TYR* 3.8 1.6 - - - -
111A HIS 3.7 1.0 - - - +
112A LEU* 3.5 10.0 - - - +
113A VAL* 2.9 68.9 + - + +
115A SER* 2.4 36.2 + - - +
130A LEU* 3.5 25.3 + - - +
131A LEU* 1.3 76.2 - - - +
133A THR* 1.3 59.8 + - - +
136A ARG 3.9 2.5 - - - -
137A THR* 3.4 24.0 - - - +
181A ILE* 3.7 18.5 - - - +
184A PHE* 3.5 24.2 - - + -
185A ASP* 2.5 45.8 + - - +
390A ARG* 4.1 7.2 - - - +
394A LEU* 4.5 3.5 - - + +
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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