Contacts of the strand formed by residues 126 - 131 (chain B) in PDB entry 2XMR
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 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PRO* 3.7 7.2 - - - -
50B ALA* 3.0 19.5 - - + +
52B LEU* 4.2 33.4 - - + -
114B ILE* 4.8 2.7 - - + -
118B LEU* 3.5 31.0 - - + -
125B THR* 1.3 79.9 - - - +
127B ILE* 1.3 61.2 + - - +
128B GLY* 4.4 9.4 - - - +
138B LEU* 4.7 5.4 - - + -
141B TYR* 3.8 29.6 - - + -
148B THR 2.8 14.6 + - - +
149B VAL* 3.6 11.0 - - + -
150B GLU* 2.8 30.3 + - - +
151B GLY 4.0 0.5 + - - +
152B LEU* 5.9 0.7 - - + -
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Residues in contact with ILE 127 (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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49B PRO* 3.5 27.6 - - + -
50B ALA 2.8 8.1 + - - +
51B ILE* 3.4 14.7 - - + +
52B LEU 2.9 23.3 + - - -
81B PHE* 4.1 12.8 - - + -
126B ILE* 1.3 73.7 - - - +
128B GLY* 1.3 65.7 + - - +
129B VAL* 3.9 1.2 + - + -
150B GLU* 4.3 0.4 - - + -
151B GLY 3.2 24.2 - - - +
153B VAL* 5.0 0.4 - - + -
293B PHE* 4.4 24.9 - - + -
296B PHE* 4.4 9.2 - - + -
297B LEU* 3.7 24.9 - - + -
300B MET* 3.7 19.5 - - + -
302B TYR* 4.4 0.2 - - + -
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Residues in contact with GLY 128 (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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52B LEU 3.3 7.9 - - - -
126B ILE* 4.0 13.9 - - - +
127B ILE* 1.3 74.2 - - - +
129B VAL* 1.3 63.4 + - - +
130B GLY 4.2 0.2 - - - -
138B LEU* 3.9 13.2 - - - -
149B VAL* 5.1 0.2 - - - +
151B GLY 3.0 9.7 + - - -
152B LEU* 3.4 14.4 - - - +
153B VAL* 2.9 25.6 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.9 25.6 - - + -
52B LEU 2.9 7.7 + - - -
53B THR* 3.1 14.0 - - + -
54B TYR 3.0 22.5 + - - -
65B PHE* 3.6 24.2 - - + -
68B LEU* 5.4 4.0 - - + -
69B PHE* 4.8 7.6 - - + -
127B ILE* 4.6 2.0 - - + +
128B GLY* 1.3 77.3 - - - +
130B GLY* 1.3 59.5 + - - +
138B LEU* 3.4 3.2 - - - +
153B VAL* 3.4 33.2 - - + -
155B ILE* 4.5 7.0 - - + -
293B PHE* 4.3 12.1 - - + -
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Residues in contact with GLY 130 (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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54B TYR 3.3 11.0 - - - -
65B PHE* 4.1 0.7 - - - -
129B VAL* 1.3 75.2 - - - +
131B VAL* 1.3 64.5 + - - -
135B ALA* 3.5 17.6 - - - +
138B LEU* 3.6 10.0 - - - +
153B VAL 3.0 9.6 + - - +
154B LEU* 5.2 0.2 - - - +
155B ILE* 2.9 31.5 + - - +
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Residues in contact with VAL 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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54B TYR 3.3 6.5 + - - -
56B ASP* 3.3 29.5 + - + +
64B CYS* 3.8 17.3 - - - -
65B PHE* 3.5 29.2 - - + -
130B GLY* 1.3 75.9 - - - +
132B GLY* 1.3 63.6 + - - +
133B ALA 3.2 1.0 + - - -
134B GLY* 2.9 17.8 + - - -
135B ALA 3.5 1.1 - - - +
155B ILE* 3.4 22.4 - - + +
156B ASN* 4.2 11.0 - - - +
280B GLN* 3.8 24.5 - - - +
282B GLN* 4.0 8.7 - - - +
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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