Contacts of the strand formed by residues 95 - 100 (chain C) in PDB entry 2ZXI
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 SER 95 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLY 2.6 21.5 + - - +
55C ILE* 2.8 27.9 + - - -
58C GLY* 3.6 0.2 - - - -
59C ILE* 3.5 18.6 + - - +
84C MET* 3.4 4.7 - - - -
85C LEU* 3.0 34.2 + - - +
93C VAL 4.0 2.8 + - - -
94C GLN* 1.3 77.4 - - - +
96C PRO* 1.3 74.5 - - - +
448C GLN* 4.5 0.4 - - - -
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Residues in contact with PRO 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLY* 3.3 5.9 - - - -
54C GLY 2.8 21.1 + - - -
58C GLY* 3.6 16.0 - - - +
62C ARG* 3.4 38.1 - - - +
83C LYS 3.6 8.5 - - - +
84C MET* 3.3 16.1 - - + -
95C SER* 1.3 92.4 - - - +
97C ARG* 1.3 57.6 + - - +
226C PRO* 4.8 5.4 - - + -
227C LYS 5.0 0.2 - - - +
228C PHE* 3.5 26.2 - - + -
448C GLN* 4.0 8.5 - - + -
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Residues in contact with ARG 97 (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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49C ASN* 4.3 4.9 + - - -
51C ALA* 3.6 15.7 - - + +
52C ILE 3.5 8.3 - - - +
53C GLY 4.3 3.2 + - - -
54C GLY* 3.8 14.6 - - - +
81C GLN* 4.3 9.2 + - - +
82C PHE* 3.5 1.2 - - - +
83C LYS* 2.9 52.7 + - + +
85C LEU* 4.1 34.8 - - + -
96C PRO* 1.3 77.5 - - - +
98C ALA* 1.3 65.8 + - - +
99C GLN* 2.7 39.9 + - - +
226C PRO* 5.5 0.2 - - - +
228C PHE* 3.7 2.2 - - - -
249C CYS* 5.4 0.4 - - - -
303C PHE* 6.0 4.6 - - - -
305C GLU* 3.3 20.2 + - - -
317C ASN* 5.1 3.8 - - - +
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Residues in contact with ALA 98 (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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51C ALA* 3.2 7.9 - - - +
52C ILE 2.8 31.7 + - - +
75C ILE* 3.7 17.7 - - + -
81C GLN* 2.9 15.9 - - - +
82C PHE* 3.5 15.7 - - + -
97C ARG* 1.3 78.2 - - - +
99C GLN* 1.3 62.1 + - - +
228C PHE* 3.4 22.0 - - + -
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Residues in contact with GLN 99 (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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50C PRO 3.3 13.9 + - - -
51C ALA* 4.1 0.4 - - - +
75C ILE* 4.4 0.4 - - - -
79C GLY* 3.4 5.2 - - - -
80C ILE* 2.8 37.6 + - + -
81C GLN* 2.8 39.7 + - + +
97C ARG* 2.7 34.4 + - - +
98C ALA* 1.3 72.9 - - - +
100C ALA* 1.3 60.0 + - - +
247C VAL* 5.4 0.9 - - + -
249C CYS* 3.5 23.8 - - - -
303C PHE* 6.0 0.7 - - - -
305C GLU* 2.7 32.9 + - - +
306C PRO* 4.4 8.5 + - + +
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Residues in contact with ALA 100 (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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46C MET* 4.0 27.8 - - + -
50C PRO* 2.7 28.6 + - - +
51C ALA* 5.0 0.2 - - - -
52C ILE* 4.8 1.6 - - + -
75C ILE* 3.4 25.4 - - + -
78C THR 4.1 2.9 - - - +
80C ILE* 4.4 6.1 - - - +
98C ALA 3.9 0.8 + - - -
99C GLN* 1.3 74.7 - - - +
101C ASP* 1.3 61.8 + - - +
102C LYS 3.1 6.6 + - - -
105C TYR* 4.5 5.8 - - + -
306C PRO 4.7 1.0 - - - +
307C GLU* 3.6 8.7 - - - +
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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