Contacts of the strand formed by residues 90 - 96 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLY 2.6 18.3 + - - +
49A MET* 3.3 13.6 - - + -
50A VAL* 2.9 25.3 + - - +
89A CYS* 1.3 78.1 - - - +
91A VAL* 1.3 63.2 + - - +
92A LEU* 4.1 12.8 - - + -
47D THR* 3.9 9.4 - - - +
48D GLY* 3.7 22.5 - - - +
49D MET* 4.0 10.3 - - + +
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Residues in contact with VAL 91 (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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50A VAL 3.5 4.3 - - - +
52A VAL* 4.8 1.8 - - + -
64A ILE* 4.6 7.0 - - + -
65A GLU* 4.0 28.3 - - + +
68A THR* 4.0 28.5 - - + +
69A ARG* 3.6 44.8 - - + +
89A CYS* 3.9 3.5 + - - -
90A ALA* 1.3 80.0 - - - +
92A LEU* 1.3 72.5 + - - +
93A SER* 4.9 1.7 + - - +
93C SER 3.7 7.1 - - - +
94C ALA* 3.8 9.9 - - - +
95C ILE 5.0 0.7 + - - -
47D THR* 4.8 1.2 + - - -
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Residues in contact with LEU 92 (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 MET* 5.1 12.3 - - + -
50A VAL 2.7 14.7 + - - +
51A LEU* 3.7 21.1 - - + -
52A VAL* 2.9 27.0 + - - +
90A ALA* 4.1 7.0 - - + -
91A VAL* 1.3 89.2 - - - +
93A SER* 1.3 64.9 + - - +
51C LEU* 4.7 7.9 - - + -
92C LEU* 3.9 23.3 - - + -
93C SER 3.3 9.9 - - - +
94C ALA* 4.1 9.0 - - + -
49D MET* 3.6 37.7 - - + -
92D LEU* 6.0 7.0 - - + -
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Residues in contact with SER 93 (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 LEU* 4.5 1.1 - - - -
52A VAL 3.1 7.5 + - - -
64A ILE* 3.7 28.4 - - - +
91A VAL* 4.9 2.6 + - - +
92A LEU* 1.3 79.7 + - - +
94A ALA* 1.3 59.8 + - - +
95A ILE* 3.7 13.0 + - - -
91C VAL 3.7 2.1 - - - +
92C LEU* 3.5 7.5 - - - -
93C SER* 3.1 42.1 + - - +
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Residues in contact with ALA 94 (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 LEU* 4.3 8.9 - - + +
52A VAL 3.0 7.5 + - - -
53A GLY* 3.1 19.3 - - - -
54A GLY 3.1 8.3 + - - +
93A SER* 1.3 74.3 - - - +
95A ILE* 1.3 58.1 + - - +
96A GLY 4.0 0.8 + - - -
44B TYR* 5.4 2.2 - - + -
46B LYS* 4.4 13.2 - - + +
49B MET* 4.1 26.9 - - + -
91C VAL 3.9 9.2 - - - +
92C LEU* 4.3 12.3 - - + -
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Residues in contact with ILE 95 (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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26A VAL* 6.1 0.2 - - + -
52A VAL* 3.5 29.6 - - + +
53A GLY* 3.6 11.9 - - - +
54A GLY 3.2 8.3 - - - +
56A ILE* 3.6 38.4 - - + +
64A ILE* 4.2 31.0 - - + -
93A SER* 3.7 10.3 - - - -
94A ALA* 1.3 74.0 - - - +
96A GLY* 1.3 71.4 + - - +
97A LYS* 5.8 0.9 + - - -
65C GLU* 4.1 12.9 - - - +
91C VAL 5.1 0.8 + - - -
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Residues in contact with GLY 96 (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 GLY 2.8 9.8 + - - -
55A GLU* 3.0 4.1 - - - -
56A ILE 2.7 32.4 + - - +
94A ALA 4.0 1.4 + - - -
95A ILE* 1.3 77.1 - - - +
97A LYS* 1.3 57.9 + - - -
46B LYS* 4.8 9.4 - - - +
47B THR* 6.0 3.8 - - - -
65C GLU* 3.3 19.5 - - - -
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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