Contacts of the strand formed by residues 132 - 141 (chain A) in PDB entry 3DOY
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 ILE 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A MET* 4.2 21.5 - - + -
127A LYS* 3.9 4.6 + - - +
128A HIS* 3.4 2.9 - - - -
129A LYS* 2.9 48.3 + - + +
130A GLY 3.2 0.2 - - - -
131A MET* 1.3 84.4 - - - +
133A TRP* 1.3 64.7 + - - +
134A GLN* 4.7 9.7 + - - +
152A LYS* 4.0 28.5 - - + -
153A ALA 3.7 2.0 - - - +
154A MET* 4.4 7.4 - - + -
2005A BEN 4.0 36.1 - - + +
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Residues in contact with TRP 133 (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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39A ASN* 3.1 32.8 - - - -
81A LEU* 5.1 0.7 - - + -
82A ALA* 3.7 42.2 - - + -
85A SER* 3.4 13.7 - - - -
86A LEU* 3.7 25.0 - - + +
125A VAL* 3.8 33.9 - - + -
127A LYS 3.6 2.9 - - - -
128A HIS* 3.5 29.6 - + + -
130A GLY 3.0 20.6 + - - -
131A MET 3.7 9.9 - - - -
132A ILE* 1.3 79.9 - - - +
134A GLN* 1.3 61.2 + - - +
135A VAL* 4.0 12.2 + - + +
151A LEU 3.9 0.7 - - - +
152A LYS* 3.2 2.2 - - - -
153A ALA* 2.6 47.1 + - + +
155A ILE* 4.0 4.9 - - + +
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Residues in contact with GLN 134 (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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125A VAL* 3.8 1.2 - - - +
126A LEU* 2.8 32.9 + - + +
127A LYS* 2.9 65.2 + - + +
132A ILE* 4.7 6.5 + - - +
133A TRP* 1.3 71.4 - - - +
135A VAL* 1.3 63.5 + - - +
150A GLU* 6.4 1.3 - - + -
151A LEU 3.4 5.8 - - - +
152A LYS* 3.4 37.2 - - + +
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Residues in contact with VAL 135 (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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74A MET 5.4 0.2 - - - +
78A GLY* 4.6 21.5 - - - +
81A LEU* 5.3 3.6 - - + -
123A LEU* 3.9 22.2 - - + -
124A GLU 3.3 14.8 - - - +
125A VAL* 4.4 15.0 - - + -
126A LEU* 3.6 5.8 - - - -
133A TRP* 4.8 13.5 - - + +
134A GLN* 1.3 81.8 - - - +
136A GLY* 1.3 59.8 + - - +
150A GLU* 3.4 3.5 - - - +
151A LEU* 2.7 65.0 + - + +
153A ALA* 6.4 0.2 - - + -
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Residues in contact with GLY 136 (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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123A LEU* 3.9 6.5 - - - -
124A GLU* 2.9 34.5 + - - +
126A LEU* 3.4 17.5 - - - +
135A VAL* 1.3 76.8 - - - +
137A GLY* 1.3 58.8 + - - -
149A ALA 3.5 10.1 - - - -
150A GLU* 4.0 4.3 - - - -
151A LEU* 6.3 0.2 - - - -
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Residues in contact with GLY 137 (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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74A MET* 3.6 5.4 - - - -
122A HIS 3.0 12.8 - - - -
123A LEU* 4.0 4.2 - - - +
124A GLU* 5.3 2.5 - - - -
136A GLY* 1.3 74.4 - - - -
138A THR* 1.3 71.4 + - - +
148A GLU* 3.7 1.4 - - - +
149A ALA 3.0 28.0 + - - +
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Residues in contact with THR 138 (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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74A MET* 3.7 9.2 - - - +
120A GLU 3.6 0.9 - - - +
121A TYR* 3.8 1.6 - - - -
122A HIS* 2.9 36.1 + - - +
137A GLY* 1.3 81.5 - - - +
139A ALA* 1.3 60.9 + - - +
140A GLN* 3.1 25.6 + - - -
145A VAL* 4.0 23.1 - - + -
147A ALA 3.3 14.8 - - - +
148A GLU* 4.0 10.1 - - + -
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Residues in contact with ALA 139 (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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70A ILE* 3.4 33.4 - - + -
74A MET* 4.1 8.9 - - + -
119A LEU* 3.8 14.8 - - + -
120A GLU 3.2 6.5 - - - +
121A TYR* 4.6 1.3 - - + +
138A THR* 1.3 73.6 - - - +
140A GLN* 1.3 61.7 + - - +
145A VAL* 3.7 0.3 - - - -
146A VAL* 2.8 33.7 + - + +
147A ALA* 2.9 13.4 + - + +
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Residues in contact with GLN 140 (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 ARG 3.3 1.7 - - - +
119A LEU* 3.8 0.5 - - - -
120A GLU* 2.7 55.8 + - - +
122A HIS* 3.6 33.0 + - + +
138A THR* 3.1 23.3 + - - +
139A ALA* 1.3 78.4 - - - +
141A VAL* 1.3 69.2 + - - +
142A ASP 4.3 0.2 - - - -
143A GLY* 3.8 21.5 - - - +
144A LYS 3.2 13.7 - - - +
145A VAL* 4.1 15.5 - - + +
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Residues in contact with VAL 141 (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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113A VAL* 4.4 4.3 - - + -
117A ASP* 3.7 40.2 - - + +
118A ARG 3.9 15.0 - - - +
119A LEU* 4.2 11.0 - - + -
140A GLN* 1.3 80.5 - - - +
142A ASP* 1.3 78.3 + - + +
143A GLY 3.2 0.2 - - - -
144A LYS* 2.9 23.4 + - - +
146A VAL* 3.6 27.8 - - + -
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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