Contacts of the strand formed by residues 71 - 77 (chain A) in PDB entry 1XPM
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ILE* 3.8 30.7 - - + -
67A ASP* 2.9 26.6 + - + +
68A LYS 4.2 0.4 + - - -
69A LYS 3.7 0.8 - - - -
70A LYS* 1.3 75.6 - - - +
72A GLY* 1.3 58.0 - - - +
73A MET 3.3 28.5 - - - +
74A VAL* 4.1 7.6 - - + -
98A ILE* 3.8 36.2 - - + +
99A GLN* 2.9 25.3 + - - +
102A ALA* 3.8 3.5 - - - +
132A LYS* 3.2 21.5 - - + +
133A VAL 5.1 0.4 - - - -
134A LEU* 4.0 13.9 - - + +
161A VAL* 5.5 2.5 - - + -
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Residues in contact with GLY 72 (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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70A LYS 3.2 4.2 + - - -
71A ILE* 1.3 71.7 - - - +
73A MET* 1.3 68.1 + - - +
99A GLN* 4.3 4.7 - - - -
101A PHE 4.3 2.8 - - - +
102A ALA* 3.1 11.9 - - - -
103A ARG* 3.0 20.8 + - - +
124A TYR* 4.1 6.8 + - - -
131A GLU* 3.5 22.4 + - - -
132A LYS 2.8 11.0 + - - -
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Residues in contact with MET 73 (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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71A ILE* 3.3 6.9 - - - +
72A GLY* 1.3 83.9 - - - +
74A VAL* 1.3 62.9 + - - +
75A ILE* 4.0 22.7 - - + -
102A ALA* 4.4 0.4 - - - -
103A ARG* 3.2 48.0 - - + +
105A PHE* 4.2 12.6 - - - -
121A ALA* 4.2 5.4 - - - +
124A TYR* 3.6 44.2 - - + -
132A LYS 4.1 2.8 + - - -
133A VAL* 3.6 18.3 - - + +
134A LEU 3.0 24.9 + - - -
120B LEU* 4.0 12.1 - - + -
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Residues in contact with VAL 74 (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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71A ILE* 4.1 5.8 - - + -
73A MET* 1.3 77.9 - - - +
75A ILE* 1.3 62.4 + - - +
76A VAL* 4.8 4.7 - - + -
89A ALA* 3.4 25.9 - - + +
92A ILE* 4.7 11.2 - - + -
93A HIS* 4.1 19.7 - - + -
98A ILE* 3.8 27.6 - - + -
102A ALA* 5.3 0.9 - - + -
103A ARG 2.8 6.5 + - - +
104A CYS* 3.3 13.7 - - - -
105A PHE 3.3 23.0 + - - -
134A LEU* 3.3 21.8 - - + +
136A ILE* 4.9 2.7 - - + -
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Residues in contact with ILE 75 (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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73A MET* 4.0 26.5 - - + -
74A VAL* 1.3 75.7 - - - +
76A VAL* 1.3 68.9 + - - +
105A PHE* 3.4 37.0 - - + +
107A MET* 3.9 31.6 - - + -
117A ALA* 3.9 38.6 - - + +
120A LEU* 5.8 0.2 - - + -
121A ALA* 5.2 0.9 - - - +
133A VAL* 4.3 7.2 - - + -
134A LEU 2.9 10.5 + - - +
135A VAL* 3.4 5.5 - - + +
136A ILE* 2.9 26.5 + - - +
120B LEU* 5.1 1.6 - - + -
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Residues in contact with VAL 76 (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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74A VAL* 4.2 4.0 - - + -
75A ILE* 1.3 78.7 - - - +
77A ALA* 1.3 66.5 + - - +
78A THR* 4.2 5.4 - - + -
88A ALA* 4.2 8.5 - - + -
89A ALA* 3.5 30.5 - - + +
92A ILE* 3.9 20.4 - - + -
105A PHE 3.1 6.3 + - - -
106A GLU* 3.1 25.4 - - + +
107A MET 2.9 23.3 + - - -
136A ILE* 3.2 10.5 - - + +
138A THR* 3.7 26.9 - - + -
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Residues in contact with ALA 77 (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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75A ILE 4.1 0.8 + - - -
76A VAL* 1.3 71.3 - - - +
78A THR* 1.3 62.7 + - - +
107A MET* 3.5 8.1 - - + +
113A ALA* 3.6 13.0 - - + +
114A ALA* 3.4 41.3 - - + +
117A ALA* 5.1 4.0 - - + -
135A VAL* 5.5 0.7 - - + -
136A ILE 2.7 12.7 + - - +
137A ALA* 4.3 0.2 - - - -
138A THR 3.0 25.1 + - - -
278A THR* 3.2 9.8 + - + +
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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