Contacts of the strand formed by residues 130 - 136 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR* 4.0 15.0 - - + -
37A PHE 3.7 4.5 - - - -
129A ASN* 1.3 73.1 - - - +
131A LEU* 1.3 66.5 + - - +
132A PHE 3.7 11.7 - - - +
133A THR* 3.6 31.0 - - + -
426A LYS* 4.4 1.2 - - - +
430A LEU* 4.1 12.8 - - + -
431A SER 4.2 5.4 - - - -
432A LEU* 3.8 28.9 - - + +
442A THR* 2.9 36.7 + - + +
458A LEU* 4.0 19.2 - - + +
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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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37A PHE* 2.9 27.3 + - + +
39A CYS* 3.8 32.1 - - + +
57A THR* 4.2 10.1 - - - +
59A PHE* 4.0 27.6 - - + -
118A ALA* 3.3 1.6 - - - +
119A VAL* 3.0 40.2 + - + +
125A ILE* 3.9 36.6 - - + -
126A PRO 5.6 0.7 - - - +
129A ASN* 3.7 11.7 - - + +
130A VAL* 1.3 80.3 - - - +
132A PHE* 1.3 65.5 + - - +
159A ILE* 4.5 3.1 - - + -
458A LEU* 4.1 3.4 - - - -
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Residues in contact with PHE 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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36A TYR* 3.3 3.3 - - - +
37A PHE* 2.8 68.0 + + + -
59A PHE* 3.7 24.7 - + - -
62A LEU* 4.5 9.6 - - + -
116A ILE* 4.2 10.3 - - + -
117A LYS 3.0 17.5 - - - +
118A ALA* 3.7 11.4 - - + +
130A VAL* 3.7 2.0 - - - +
131A LEU* 1.3 79.7 - - - +
133A THR* 1.3 64.4 + - - +
134A VAL* 3.9 25.8 - - + -
152A LEU* 4.1 29.8 - - + -
155A SER* 3.7 19.7 - - - -
399A PHE* 4.1 5.4 - + - -
458A LEU* 4.7 1.1 - - - -
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Residues in contact with THR 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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34A TYR* 3.5 35.2 + - + +
35A SER 3.2 8.1 - - - -
36A TYR* 3.9 9.9 - - + +
115A GLU 3.8 0.8 - - - +
116A ILE* 3.1 11.1 - - - +
117A LYS* 2.8 50.9 + - - +
130A VAL* 3.6 21.1 - - + -
132A PHE* 1.3 76.6 - - - +
134A VAL* 1.3 64.2 + - - +
135A GLU* 5.1 2.8 + - - -
430A LEU* 4.6 2.9 - - + -
458A LEU* 4.1 11.1 - - + +
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Residues in contact with VAL 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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34A TYR* 3.4 4.4 - - - +
35A SER 2.7 38.0 + - - +
114A ILE* 3.8 15.9 - - + -
115A GLU 3.5 3.1 - - - -
116A ILE* 4.0 6.3 - - + -
132A PHE* 3.9 10.3 - - + -
133A THR* 1.3 81.1 - - - +
135A GLU* 1.3 64.1 + - - +
145A THR* 3.4 19.5 - - + +
148A ILE* 3.8 26.2 - - + -
152A LEU* 3.6 24.0 - - + -
399A PHE* 3.8 22.7 - - + -
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Residues in contact with GLU 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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32A LYS* 3.0 33.3 + - + +
33A VAL 3.6 11.2 - - - +
34A TYR* 4.0 30.8 - - + -
114A ILE* 3.2 7.7 - - - +
115A GLU* 2.8 65.3 + - + +
117A LYS* 4.4 16.6 + - - +
133A THR* 5.1 2.9 + - - -
134A VAL* 1.3 75.8 - - - +
136A ASN* 1.3 60.7 + - - +
137A THR* 5.2 1.1 - - + -
145A THR* 3.6 4.0 - - - -
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Residues in contact with ASN 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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31A SER 3.0 23.4 + - - -
32A LYS* 3.0 29.5 + - - +
33A VAL 2.9 29.5 + - - +
113A PRO 3.4 9.6 - - - +
114A ILE* 4.1 4.5 - - + -
135A GLU* 1.3 74.2 - - - +
137A THR* 1.3 61.3 + - - +
138A ASP 2.9 24.0 + - - +
141A CYS* 3.2 21.3 - - + +
142A TYR* 3.6 16.4 - - - +
145A THR* 3.1 9.1 + - - +
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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