Contacts of the strand formed by residues 130 - 136 (chain B) in PDB entry 3DGR
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 VAL 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B TYR* 4.0 16.2 - - + -
37B PHE 3.7 4.3 - - - -
129B ASN* 1.3 71.1 - - - +
131B LEU* 1.3 66.6 + - - +
132B PHE 3.9 10.3 - - - +
133B THR* 3.6 31.2 - - + -
426B LYS* 4.4 1.6 - - - +
430B LEU* 4.0 13.5 - - + -
431B SER 4.1 8.7 - - - -
432B LEU* 4.0 27.0 - - + +
442B THR* 2.9 36.0 + - + +
458B LEU* 4.0 16.6 - - + +
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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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37B PHE* 2.8 29.9 + - + +
39B CYS* 3.8 33.4 - - + +
57B THR* 4.1 10.8 - - - +
59B PHE* 4.0 28.0 - - + -
118B ALA* 3.5 1.2 - - - +
119B VAL* 3.1 39.4 + - + +
125B ILE* 4.1 34.1 - - + -
126B PRO 5.6 0.4 - - - +
129B ASN* 3.6 12.6 - - + +
130B VAL* 1.3 79.1 - - - +
132B PHE* 1.3 64.6 + - - +
159B ILE* 4.7 2.7 - - + -
458B LEU* 4.3 3.4 - - - -
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Residues in contact with PHE 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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36B TYR* 3.3 3.6 - - - +
37B PHE* 2.8 71.3 + + + -
59B PHE* 3.7 25.8 - + - -
62B LEU* 4.3 13.5 - - + -
116B ILE* 4.3 7.6 - - + -
117B LYS 3.0 17.7 - - - +
118B ALA* 3.8 12.3 - - + +
130B VAL* 3.7 1.8 - - - +
131B LEU* 1.3 80.3 - - - +
133B THR* 1.3 65.8 + - - +
134B VAL* 3.9 25.4 - - + -
152B LEU* 4.0 33.4 - - + -
155B SER* 3.7 15.0 - - - -
399B PHE* 4.2 6.5 - + - -
458B LEU* 5.0 0.7 - - - -
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Residues in contact with THR 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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34B TYR* 3.4 35.6 + - + +
35B SER 3.3 8.1 - - - -
36B TYR* 4.1 7.2 - - + -
115B GLU 3.6 0.6 + - - +
116B ILE* 3.1 10.2 - - - +
117B LYS* 2.8 52.3 + - - +
130B VAL* 3.6 22.7 - - + -
132B PHE* 1.3 77.7 - - - +
134B VAL* 1.3 64.0 + - - +
135B GLU* 4.9 2.4 + - - -
430B LEU* 4.7 2.5 - - + +
458B LEU* 3.9 11.4 - - + +
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Residues in contact with VAL 134 (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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34B TYR* 3.4 5.0 - - - -
35B SER 2.8 35.8 + - - +
114B ILE* 3.8 14.4 - - + -
115B GLU 3.5 2.5 - - - -
116B ILE* 4.1 6.3 - - + -
132B PHE* 3.9 12.3 - - + -
133B THR* 1.3 82.3 - - - +
135B GLU* 1.3 63.4 + - - +
145B THR* 3.5 23.9 - - + +
148B ILE* 3.8 27.8 - - + -
152B LEU* 3.6 23.3 - - + -
399B PHE* 3.8 17.3 - - + -
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Residues in contact with GLU 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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32B LYS* 2.9 35.3 + - + +
33B VAL 3.5 13.0 - - - +
34B TYR* 3.9 31.5 - - + -
114B ILE* 3.3 6.1 - - - +
115B GLU* 2.7 61.4 + - + +
117B LYS* 4.3 19.9 + - - +
133B THR* 4.9 3.1 + - - -
134B VAL* 1.3 76.0 - - - +
136B ASN* 1.3 60.2 + - - +
137B THR* 5.1 0.7 - - + -
145B THR* 3.8 4.3 - - - -
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Residues in contact with ASN 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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31B SER 2.9 18.2 - - - +
32B LYS* 3.1 30.0 + - - +
33B VAL 3.0 35.0 + - - +
113B PRO 3.5 10.5 - - - +
114B ILE* 4.4 2.0 - - - +
135B GLU* 1.3 73.7 - - - +
137B THR* 1.3 59.8 + - - +
138B ASP 2.8 21.8 - - - +
141B CYS* 3.2 22.7 - - + +
142B TYR* 3.5 13.9 + - - +
144B LEU* 5.0 2.2 - - + -
145B THR* 3.3 8.6 + - - +
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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