Contacts of the strand formed by residues 90 - 96 (chain B) in PDB entry 1P7L
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 ALA 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B GLY 2.6 17.4 + - - +
49B MET* 3.3 14.5 - - + -
50B VAL* 2.9 25.2 + - - +
89B CYS* 1.3 79.3 - - - +
91B VAL* 1.3 63.9 + - - +
92B LEU* 4.0 13.0 - - + -
47C THR* 3.9 9.0 - - - +
48C GLY* 3.8 21.3 - - - +
49C MET* 4.1 9.9 - - + -
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Residues in contact with VAL 91 (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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50B VAL 3.6 3.6 - - - +
52B VAL* 4.8 1.6 - - + -
64B ILE* 4.6 6.5 - - + -
65B GLU* 3.9 29.4 - - + +
68B THR* 4.0 27.8 - - + +
69B ARG* 3.6 45.3 - - + +
89B CYS* 3.9 3.5 + - - -
90B ALA* 1.3 79.5 - - - +
92B LEU* 1.3 73.4 + - - +
93B SER* 5.0 1.7 + - - +
47C THR* 4.8 1.0 + - - -
93D SER 3.6 7.6 - - - +
94D ALA* 3.8 10.2 - - - +
95D ILE 4.9 0.9 + - - -
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Residues in contact with LEU 92 (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 MET* 5.1 11.7 - - + -
50B VAL 2.7 17.2 + - - +
51B LEU* 3.8 17.9 - - + -
52B VAL* 2.9 27.9 + - - +
90B ALA* 4.0 13.9 - - + -
91B VAL* 1.3 83.2 - - - +
93B SER* 1.3 64.6 + - - +
49C MET* 3.7 37.9 - - + -
92C LEU* 6.0 6.1 - - + -
51D LEU* 4.8 4.3 - - + -
92D LEU* 3.8 27.4 - - + -
93D SER 3.3 9.9 - - - +
94D ALA* 4.1 9.4 - - + -
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Residues in contact with SER 93 (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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51B LEU* 4.5 2.0 - - - -
52B VAL 3.1 8.0 + - - -
64B ILE* 3.8 27.6 - - - +
91B VAL* 5.0 2.8 + - - +
92B LEU* 1.3 78.8 + - - +
94B ALA* 1.3 60.4 + - - +
95B ILE* 3.8 13.2 - - - -
91D VAL 3.6 2.3 - - - +
92D LEU* 3.4 7.9 - - - -
93D SER* 3.0 42.8 + - - +
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Residues in contact with ALA 94 (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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44A TYR* 5.4 2.5 - - + -
46A LYS* 4.4 12.9 - - + +
49A MET* 4.2 25.8 - - + -
51B LEU* 4.3 9.1 - - + +
52B VAL 3.0 7.5 + - - -
53B GLY* 3.1 6.4 - - - -
54B GLY 3.1 21.3 + - - +
93B SER* 1.3 73.9 - - - +
95B ILE* 1.3 58.8 + - - +
96B GLY 4.0 1.0 + - - -
91D VAL 3.9 13.9 - - - +
92D LEU* 4.4 7.9 - - + -
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Residues in contact with ILE 95 (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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26B VAL* 6.0 0.2 - - + -
41B CYS* 5.9 0.2 - - - -
52B VAL* 3.6 30.7 - - + +
53B GLY* 3.8 9.4 - - - +
54B GLY 3.3 8.5 - - - +
56B ILE* 3.7 39.0 - - + +
64B ILE* 4.2 30.7 - - + -
93B SER* 3.8 10.5 - - - -
94B ALA* 1.3 73.0 - - - +
96B GLY* 1.3 72.3 - - - +
97B LYS* 5.7 1.2 + - - -
65D GLU* 4.0 13.5 - - - +
91D VAL 5.1 0.8 + - - -
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Residues in contact with GLY 96 (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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46A LYS* 4.7 9.8 - - - +
47A THR* 6.0 2.9 - - - -
54B GLY 2.8 10.0 + - - -
55B GLU* 3.1 4.1 - - - -
56B ILE 2.7 32.1 + - - +
94B ALA 4.0 1.4 + - - -
95B ILE* 1.3 77.5 - - - +
97B LYS* 1.3 58.4 + - - -
65D GLU* 3.3 20.0 - - - -
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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