Contacts of the strand formed by residues 90 - 96 (chain A) in PDB entry 6ZGI
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 VAL 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A PRO 4.4 0.2 - - - +
86A PHE* 3.7 31.6 - - + -
89A GLY* 1.3 80.1 - - - +
91A TYR* 1.3 77.2 + - - +
92A PHE* 4.0 10.7 + - + +
192A PHE 3.8 0.5 - - - +
193A VAL* 3.4 5.9 - - - +
194A PHE* 2.9 39.8 + - + +
238A PHE* 3.8 24.5 - - + -
267A VAL* 4.1 13.5 - - + -
268A GLY 3.7 6.1 - - - +
269A TYR* 4.2 15.9 - - + -
270A LEU* 4.0 4.2 - - - +
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Residues in contact with TYR 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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31A SER* 6.0 0.4 - - - -
34A ARG* 3.9 18.1 - - + +
35A GLY* 3.6 28.9 - - - -
56A LEU* 3.9 26.5 - - + -
62A VAL* 5.4 4.9 - - + -
90A VAL* 1.3 73.4 - - - +
92A PHE* 1.3 58.5 - - - +
93A ALA* 3.6 27.2 - - + +
191A GLU* 3.0 45.5 + - + +
192A PHE 3.6 10.8 - - - -
193A VAL* 4.0 8.7 - - + -
216A LEU* 4.9 9.0 - - + +
223A LEU* 4.8 2.2 - - + -
266A TYR* 4.9 3.8 - - + -
267A VAL* 3.6 4.5 - - - -
268A GLY* 2.9 43.0 + - - +
270A LEU* 4.2 15.2 - - + +
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Residues in contact with PHE 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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90A VAL* 3.9 5.8 - - + -
91A TYR* 1.3 74.8 - - - +
93A ALA* 1.3 62.7 + - - +
94A SER* 4.0 21.3 - - - -
101A ILE* 4.2 15.3 - - + -
104A TRP* 3.7 42.4 - + - -
190A ARG 3.7 0.5 - - - +
191A GLU* 3.5 1.9 - - - +
192A PHE* 2.9 46.3 + + + +
194A PHE* 4.2 17.3 - + + -
238A PHE* 4.8 8.5 - + - -
240A THR* 3.9 12.6 - - + -
265A TYR* 3.5 40.4 - + + -
266A TYR 3.6 2.0 - - - -
267A VAL* 4.2 14.6 - - + -
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Residues in contact with ALA 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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91A TYR* 3.6 30.2 - - + +
92A PHE* 1.3 77.3 - - - +
94A SER* 1.3 62.0 + - - +
189A LEU* 4.4 1.6 - - + -
190A ARG 3.5 4.0 - - - -
191A GLU* 4.4 6.3 - - + +
216A LEU* 4.1 22.0 - - + -
265A TYR* 3.2 6.2 - - - +
266A TYR* 2.9 40.6 + - + +
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Residues in contact with SER 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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92A PHE* 4.0 17.5 - - - -
93A ALA* 1.3 77.0 - - - +
95A THR* 1.3 62.1 + - - +
96A GLU* 3.7 13.0 + - - +
101A ILE* 3.4 28.0 - - - +
188A ASN 3.4 2.3 - - - +
189A LEU* 3.3 7.2 - - - +
190A ARG* 2.9 45.9 + - - +
192A PHE* 5.8 1.3 - - - -
264A ALA 3.6 5.2 - - - -
265A TYR* 4.6 1.1 - - - -
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Residues in contact with THR 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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93A ALA 4.4 0.2 - - - -
94A SER* 1.3 73.1 - - - +
96A GLU* 1.3 61.3 + - - +
186A PHE* 4.0 26.3 - - - -
188A ASN 3.5 4.0 - - - -
189A LEU* 3.8 19.7 - - + -
210A ILE* 4.2 12.8 - - + -
212A LEU* 4.8 8.7 - - + -
216A LEU* 4.9 3.8 - - + -
217A PRO* 5.0 3.6 - - + -
263A ALA* 3.9 2.3 - - - -
264A ALA* 2.9 47.8 + - - +
266A TYR* 3.8 21.2 + - + +
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Residues in contact with GLU 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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94A SER* 3.7 10.3 - - - +
95A THR* 1.3 74.3 - - - +
97A LYS* 1.3 62.7 + - - +
98A SER 4.4 2.5 - - - +
99A ASN* 3.5 7.2 - - - +
100A ILE* 2.8 15.6 + - + +
101A ILE* 2.3 62.6 + - + +
186A PHE* 4.1 8.7 - - - -
187A LYS 3.2 4.9 + - - -
188A ASN* 2.9 38.1 + - + +
190A ARG* 3.5 33.6 + - - +
263A ALA* 4.2 7.2 - - + -
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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