Contacts of the strand formed by residues 90 - 96 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B THR* 3.9 9.4 - - - +
48B GLY* 3.8 20.7 - - - +
49B MET* 3.9 17.5 - - + -
48C GLY 2.6 19.1 + - - +
49C MET* 3.4 10.8 - - + -
50C VAL* 3.0 23.6 + - - +
89C CYS* 1.3 78.3 - - - +
91C VAL* 1.3 63.4 + - - +
92C LEU* 4.0 11.0 - - + -
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER 3.7 8.5 - - - +
94A ALA* 3.9 9.9 - - - +
95A ILE 5.1 0.5 + - - -
47B THR* 4.8 0.8 + - - -
50C VAL 3.5 4.9 - - - +
52C VAL* 4.9 1.3 - - + -
64C ILE* 4.5 7.0 - - + -
65C GLU* 3.9 29.4 - - + +
68C THR* 4.1 26.7 - - + +
69C ARG* 3.7 43.7 - - + +
89C CYS* 4.0 4.0 + - - -
90C ALA* 1.3 78.4 - - - +
92C LEU* 1.3 72.4 + - - +
93C SER* 5.0 1.9 + - - +
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Residues in contact with LEU 92 (chain C).
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* 4.7 8.7 - - + -
92A LEU* 3.9 22.9 - - + -
93A SER 3.5 9.2 - - - +
94A ALA* 4.3 9.4 - - + -
49B MET* 3.5 37.0 - - + -
92B LEU* 6.0 6.5 - - + -
49C MET* 5.1 12.3 - - + -
50C VAL 2.7 13.4 + - - +
51C LEU* 3.8 22.7 - - + -
52C VAL* 2.9 26.2 + - - +
90C ALA* 4.0 6.7 - - + -
91C VAL* 1.3 86.9 - - - +
93C SER* 1.3 65.9 + - - +
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL 3.7 1.2 - - - +
92A LEU* 3.3 9.5 - - - +
93A SER* 3.1 43.4 + - - +
51C LEU* 4.5 1.6 - - - -
52C VAL 3.1 8.9 + - - -
64C ILE* 3.6 28.5 - - - +
91C VAL* 5.0 2.3 + - - +
92C LEU* 1.3 79.2 + - - +
94C ALA* 1.3 60.0 + - - +
95C ILE* 3.8 12.1 - - - -
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL 3.8 10.1 - - - +
92A LEU* 4.1 12.6 - - + -
51C LEU* 4.3 7.1 - - + +
52C VAL 3.0 6.7 + - - -
53C GLY* 3.2 5.6 - - - -
54C GLY 3.2 20.3 + - - +
93C SER* 1.3 73.2 - - - +
95C ILE* 1.3 59.4 + - - +
96C GLY 3.9 0.7 + - - -
44D TYR* 5.3 1.1 - - + -
46D LYS* 4.1 15.2 - - + +
47D THR* 6.1 1.1 - - - +
49D MET* 4.0 28.5 - - + -
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU* 4.2 11.8 - - - +
91A VAL 5.0 0.8 + - - -
52C VAL* 3.3 31.0 - - + +
53C GLY* 3.7 9.6 - - - +
54C GLY 3.4 7.0 - - - +
56C ILE* 3.7 36.6 - - + +
64C ILE* 4.1 31.4 - - + -
93C SER* 3.8 10.1 - - - +
94C ALA* 1.3 74.2 - - - +
96C GLY* 1.3 72.0 + - - +
97C LYS* 5.9 0.5 + - - -
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Residues in contact with GLY 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU* 3.4 17.9 - - - -
54C GLY 2.8 11.6 + - - -
55C GLU* 3.8 3.4 - - - -
56C ILE 2.6 34.3 + - - +
94C ALA 3.9 1.8 + - - -
95C ILE* 1.3 76.7 - - - +
97C LYS* 1.3 58.5 + - - -
46D LYS* 4.6 9.0 - - - +
47D THR* 5.8 3.3 - - - +
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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