Contacts of the strand formed by residues 91 - 99 (chain A) in PDB entry 4ZIN
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 PHE 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A CH6 5.7 0.4 - - - -
70A LYS* 4.2 17.9 - - + -
71A ALA* 4.6 4.5 - - + -
83A LEU* 3.7 44.0 - - + -
86A SER* 3.5 16.6 - - - +
87A PHE* 3.7 27.4 - + - -
90A GLY* 1.3 75.6 - - - +
92A LYS* 1.3 77.8 + - - +
93A TRP* 3.7 24.5 - + - -
111A SER* 2.9 48.5 + - - +
120A TYR* 5.7 2.0 - + - -
181A TYR* 4.6 2.9 - + + -
182A LYS 3.3 15.9 - - - +
183A ALA* 3.7 7.6 - - - -
184A LYS* 3.7 7.4 - - - +
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Residues in contact with LYS 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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91A PHE* 1.3 81.1 - - - +
93A TRP* 1.3 67.9 + - - +
109A GLN* 3.2 12.8 - - - +
110A ASP* 2.9 36.0 + - + +
181A TYR* 3.5 1.0 - - - -
182A LYS* 2.8 38.2 + - + +
184A LYS* 3.8 19.9 - - + +
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Residues in contact with TRP 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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64A GLN* 3.6 19.5 - - + -
66A CH6 3.7 32.6 + - - -
70A LYS* 5.3 0.9 - - + +
91A PHE* 3.7 21.7 - + - -
92A LYS* 1.3 78.0 - - - +
94A GLU* 1.3 62.0 + - - +
95A ARG* 3.6 40.6 - - + -
107A VAL* 3.6 28.5 - - + -
108A THR* 3.3 4.7 - - - -
109A GLN* 2.9 78.6 + - + +
179A THR* 3.8 16.2 - - + -
180A THR 3.1 12.3 - - - +
181A TYR* 3.6 23.0 - + + -
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Residues in contact with GLU 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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93A TRP* 1.3 76.2 - - - +
95A ARG* 1.3 64.9 + - - +
96A VAL* 5.9 3.8 - - + -
107A VAL 3.3 9.0 - - - +
108A THR* 4.0 18.0 - - + +
178A LYS 4.0 0.7 - - - +
179A THR* 3.3 2.3 - - - -
180A THR* 2.9 41.4 + - - +
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Residues in contact with ARG 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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63A PRO* 2.9 27.3 + - - +
64A GLN* 2.9 35.9 + - - -
66A CH6 2.7 30.2 + - - +
93A TRP* 3.6 25.6 - - + -
94A GLU* 1.3 76.6 - - - +
96A VAL* 1.3 68.7 + - - +
97A MET* 4.0 16.4 - - + -
106A THR* 3.3 6.2 - - - -
107A VAL* 2.8 36.7 + - + +
148A GLU* 4.8 1.4 + - - -
161A ILE* 5.6 2.3 - - - +
177A VAL* 3.7 24.2 - - + +
178A LYS 3.4 4.0 - - - -
179A THR* 2.9 20.5 + - - +
181A TYR* 3.1 26.1 + - - -
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Residues in contact with VAL 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 GLU* 5.9 3.1 - - + -
95A ARG* 1.3 79.0 - - - +
97A MET* 1.3 67.9 + - - +
98A ASN* 4.3 22.4 - - - +
104A VAL* 4.9 4.7 - - + -
105A VAL 3.5 5.8 - - - +
106A THR* 4.3 15.9 - - + -
176A GLU 3.9 0.9 - - - +
177A VAL* 3.4 3.5 - - - +
178A LYS* 3.0 37.3 + - + +
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Residues in contact with MET 97 (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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60A ILE 4.6 2.9 - - - +
63A PRO* 5.0 4.3 - - + -
64A GLN* 3.5 27.6 - - - +
95A ARG* 4.0 10.3 - - + -
96A VAL* 1.3 77.0 - - - +
98A ASN* 1.3 62.0 - - - +
99A PHE* 3.6 18.2 + - + -
104A VAL* 3.3 10.6 - - - +
105A VAL* 2.8 52.1 + - + +
143A 4OO 3.1 36.8 - - - +
163A GLN* 5.1 2.5 - - + +
175A ALA* 4.9 1.6 - - + -
176A GLU 3.4 4.5 - - - -
177A VAL* 3.9 29.8 - - + -
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Residues in contact with ASN 98 (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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96A VAL* 4.2 15.4 - - - +
97A MET* 1.3 72.2 - - - +
99A PHE* 1.3 66.7 + - - +
100A GLU 3.9 0.2 + - - -
103A GLY 3.9 0.6 - - - +
104A VAL* 3.6 24.1 - - - +
175A ALA* 3.3 2.1 - - - -
176A GLU* 2.8 53.5 + - + +
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Residues in contact with PHE 99 (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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60A ILE* 3.9 20.2 - - + -
97A MET* 3.6 31.4 - - + -
98A ASN* 1.3 77.3 - - - +
100A GLU* 1.3 67.0 + - - +
101A ASP* 3.2 4.0 - - - +
102A GLY* 3.0 16.1 + - - -
103A GLY 2.9 23.7 + - - +
105A VAL* 3.7 18.8 - - + -
129A PHE* 3.7 11.4 - + - -
143A 4OO 3.1 32.1 - - - -
165A LEU* 4.6 2.9 - - + -
173A TYR* 3.3 44.6 - + - +
174A ASP 3.6 4.7 - - - -
175A ALA* 3.7 11.9 - - + -
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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