Contacts of the strand formed by residues 132 - 141 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B MET* 4.7 17.0 - - + -
127B LYS 4.3 0.3 - - - +
128B HIS* 3.3 2.4 - - - -
129B LYS* 3.0 38.6 + - + +
130B GLY 3.3 0.4 - - - -
131B MET* 1.3 81.9 - - + +
133B TRP* 1.3 64.0 + - - +
134B GLN* 4.7 9.2 + - - +
152B LYS* 3.9 32.3 - - + -
153B ALA 3.6 5.6 - - - +
154B MET* 4.4 19.1 - - + -
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Residues in contact with TRP 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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39B ASN* 3.3 35.4 - - - -
82B ALA* 4.0 27.4 - - + -
85B SER* 3.8 14.1 - - - -
86B LEU* 3.7 35.7 - - + +
125B VAL* 3.8 36.3 - - + -
127B LYS 3.8 2.7 - - - -
128B HIS* 3.4 29.5 - + + +
130B GLY 3.3 17.5 + - - -
131B MET 3.8 13.6 + - - -
132B ILE* 1.3 80.8 - - - +
134B GLN* 1.3 61.1 + - - +
135B VAL* 4.1 9.0 + - + +
151B LEU 4.0 0.3 - - - +
152B LYS* 3.4 2.3 - - - -
153B ALA* 2.8 43.9 + - + +
155B ILE* 4.2 9.4 - - + -
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 3.6 3.0 - - - +
126B LEU* 2.7 41.6 + - + +
127B LYS* 2.8 66.1 + - + +
128B HIS* 6.1 0.2 - - - +
132B ILE* 4.7 8.5 + - + +
133B TRP* 1.3 72.2 - - - +
135B VAL* 1.3 56.1 + - - +
151B LEU 3.3 6.7 - - - +
152B LYS* 3.5 38.1 - - + +
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Residues in contact with VAL 135 (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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74B MET 5.2 0.9 - - - +
78B GLY* 4.2 30.3 - - - +
81B LEU* 4.5 4.0 - - + -
82B ALA* 5.8 0.4 - - + -
101B PHE* 5.0 6.3 - - + -
123B LEU* 3.9 22.0 - - + -
124B GLU 3.2 15.0 - - - +
125B VAL* 4.3 15.3 - - + -
126B LEU* 3.8 8.6 - - - +
133B TRP* 4.1 11.4 - - + +
134B GLN* 1.3 82.2 - - - +
136B GLY* 1.3 60.2 + - - +
150B GLU* 3.5 1.9 - - - -
151B LEU* 2.8 50.0 + - + +
153B ALA 6.3 0.2 - - - +
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Residues in contact with GLY 136 (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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123B LEU* 3.4 8.2 - - - -
124B GLU* 2.9 40.7 + - - +
126B LEU* 3.9 13.6 - - - +
135B VAL* 1.3 77.4 - - - +
137B GLY* 1.3 58.9 + - - -
149B ALA 3.2 12.8 - - - -
150B GLU* 4.1 4.9 - - - -
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Residues in contact with GLY 137 (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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74B MET* 3.6 5.6 - - - -
122B HIS 3.0 11.0 - - - -
123B LEU* 3.9 1.6 - - - +
124B GLU* 5.5 3.4 - - - -
136B GLY* 1.3 75.7 - - - -
138B THR* 1.3 67.7 + - - +
148B GLU* 3.3 6.2 - - - +
149B ALA 3.0 27.9 + - - +
150B GLU* 5.3 0.4 - - - +
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Residues in contact with THR 138 (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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74B MET* 3.5 12.7 - - - +
120B GLU 3.8 0.2 - - - +
121B TYR* 3.7 0.9 - - - -
122B HIS* 2.8 37.4 + - - +
137B GLY* 1.3 81.2 - - - +
139B ALA* 1.3 62.9 + - - +
140B GLN* 3.0 25.8 + - - -
145B VAL* 4.0 21.0 - - + +
147B ALA 3.2 14.6 - - - +
148B GLU* 3.8 13.0 - - + +
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Residues in contact with ALA 139 (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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70B ILE* 3.5 32.1 - - + -
74B MET* 4.1 8.7 - - + +
119B LEU* 4.1 7.4 - - + -
120B GLU 3.3 6.3 - - - +
121B TYR* 4.7 2.5 - - + +
138B THR* 1.3 74.5 - - - +
140B GLN* 1.3 62.8 + - - +
145B VAL* 3.7 0.5 - - - -
146B VAL* 2.8 38.6 + - + -
147B ALA* 2.9 15.2 + - + +
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Residues in contact with GLN 140 (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 ARG 3.4 1.9 - - - +
119B LEU* 4.6 0.4 - - - +
120B GLU* 2.7 48.4 + - - +
122B HIS* 3.3 41.4 + - + +
138B THR* 3.0 23.3 + - - +
139B ALA* 1.3 79.6 - - - +
141B VAL* 1.3 66.5 + - - +
142B ASP 4.1 0.8 + - - -
143B GLY* 4.0 21.0 - - - +
144B LYS 3.1 15.7 - - - +
145B VAL* 4.1 12.8 - - - +
146B VAL 4.3 0.4 - - - +
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Residues in contact with VAL 141 (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 PRO 6.0 0.2 - - - +
113B VAL* 4.3 7.2 - - + -
117B ASP* 3.6 43.3 - - + +
118B ARG 3.8 11.2 - - - +
119B LEU* 4.0 18.6 - - + -
140B GLN* 1.3 76.8 - - - +
142B ASP* 1.3 78.9 + - + +
144B LYS* 3.0 24.1 + - - +
146B VAL* 3.6 22.4 - - + +
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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