Contacts of the strand formed by residues 126 - 131 (chain A) in PDB entry 2XMS
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PRO* 3.6 7.0 - - - -
50A ALA* 3.1 17.0 - - + +
52A LEU* 4.1 33.2 - - + -
114A ILE* 5.0 2.2 - - + -
118A LEU* 3.6 32.8 - - + -
125A THR* 1.3 80.2 - - - +
127A ILE* 1.3 59.3 + - - +
128A GLY* 4.3 16.6 - - - +
138A LEU* 4.7 4.9 - - + -
141A TYR* 4.1 25.1 - - + -
148A THR 2.9 14.1 + - - +
149A VAL* 3.7 11.2 - - + -
150A GLU* 2.8 30.7 + - - +
151A GLY 4.1 0.2 - - - +
152A LEU* 5.5 1.3 - - + -
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Residues in contact with ILE 127 (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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49A PRO* 3.5 27.4 - - + -
50A ALA 2.8 8.7 + - - +
51A ILE* 3.5 12.8 - - + +
52A LEU 3.0 23.0 + - - +
81A PHE* 4.2 9.9 - - + -
126A ILE* 1.3 73.7 - - - +
128A GLY* 1.3 69.4 + - - +
129A VAL* 3.8 3.3 + - + -
150A GLU* 4.2 0.2 - - + -
151A GLY 3.3 20.0 - - - +
152A LEU 4.6 0.2 - - - +
153A VAL* 4.9 0.9 - - + -
293A PHE* 4.3 22.7 - - + -
296A PHE* 4.4 8.7 - - + -
297A LEU* 3.6 28.7 - - + -
300A MET* 3.9 21.5 - - + -
302A TYR* 5.0 0.9 - - + -
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Residues in contact with GLY 128 (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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52A LEU 3.2 8.1 - - - -
126A ILE* 4.0 13.4 - - - +
127A ILE* 1.3 74.9 - - - +
129A VAL* 1.3 56.5 + - - +
130A GLY 4.1 0.2 - - - -
138A LEU* 3.9 10.1 - - - -
151A GLY 3.0 9.3 + - - -
152A LEU* 3.3 17.9 - - - +
153A VAL 2.7 33.0 + - - +
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Residues in contact with VAL 129 (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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51A ILE* 4.0 24.5 - - + -
52A LEU 2.8 8.9 + - - -
53A THR* 3.2 14.2 - - + -
54A TYR 3.1 22.0 + - - -
65A PHE* 3.7 21.7 - - + -
68A LEU* 4.9 10.8 - - + -
69A PHE* 4.8 5.6 - - + -
127A ILE* 4.4 2.5 - - + +
128A GLY* 1.3 77.9 - - - +
130A GLY* 1.3 59.8 + - - +
138A LEU* 3.4 3.1 - - - +
153A VAL* 3.3 33.4 - - + +
155A ILE* 4.3 9.2 - - + -
293A PHE* 4.6 11.2 - - + -
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Residues in contact with GLY 130 (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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54A TYR 3.3 9.4 - - - -
65A PHE* 4.4 0.2 - - - -
129A VAL* 1.3 75.9 - - - +
131A VAL* 1.3 62.8 + - - -
135A ALA* 3.6 19.1 - - - +
138A LEU* 3.6 11.5 - - - +
153A VAL 2.9 10.1 + - - +
154A LEU* 4.9 0.2 - - - +
155A ILE* 2.9 30.7 + - - +
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Residues in contact with VAL 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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54A TYR 3.3 6.1 + - - -
56A ASP* 3.2 28.4 + - + +
64A CYS* 3.6 27.4 - - - -
65A PHE* 3.8 15.5 - - + -
130A GLY* 1.3 77.3 - - - +
132A GLY* 1.3 68.8 + - - +
133A ALA 3.2 1.4 + - - -
134A GLY 3.0 11.3 + - - -
135A ALA 3.6 0.9 - - - +
155A ILE* 3.4 20.4 - - + -
156A ASN* 4.1 11.0 - - - +
280A GLN* 3.8 23.6 - - - +
282A GLN* 3.9 13.5 - - - +
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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