Contacts of the strand formed by residues 91 - 99 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C CH6 5.7 0.4 - - - -
70C LYS* 4.3 24.7 - - + -
71C ALA* 4.7 4.0 - - + -
83C LEU* 3.8 34.5 - - + -
86C SER* 3.5 15.3 - - - +
87C PHE* 3.4 28.3 - + - -
90C GLY* 1.3 75.6 - - - +
92C LYS* 1.3 74.9 + - - +
93C TRP* 3.5 26.5 - + + -
110C ASP* 3.9 0.2 - - - -
111C SER* 3.0 46.7 + - - +
120C TYR* 5.6 2.2 - + - -
181C TYR* 4.6 1.8 - + + -
182C LYS 3.2 20.9 - - - +
183C ALA* 3.9 3.8 - - - -
184C LYS* 3.7 8.2 - - - +
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Residues in contact with LYS 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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91C PHE* 1.3 82.3 - - - +
93C TRP* 1.3 63.2 + - - +
94C GLU* 5.9 5.6 - - + +
109C GLN 3.1 12.8 - - - +
110C ASP* 3.5 27.4 + - + +
180C THR 3.9 0.2 - - - +
181C TYR* 3.6 0.9 - - - -
182C LYS* 3.0 35.1 + - + +
184C LYS* 4.3 14.6 - - + +
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Residues in contact with TRP 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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64C GLN* 3.7 18.6 - - - -
66C CH6 3.6 33.3 + - - -
70C LYS* 5.2 0.6 - - + +
91C PHE* 3.5 22.9 - + - -
92C LYS* 1.3 74.8 - - - +
94C GLU* 1.3 68.1 + - - +
95C ARG* 3.6 48.9 - - + -
107C VAL* 3.5 27.8 - - + -
108C THR* 3.3 4.0 - - - -
109C GLN* 2.8 79.5 + - + +
122C VAL* 5.0 0.2 - - + -
179C THR* 4.0 7.9 - - + -
180C THR 3.1 13.7 - - - +
181C TYR* 3.6 21.0 - + + -
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Residues in contact with GLU 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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92C LYS* 5.6 6.5 - - + +
93C TRP* 1.3 82.1 - - - +
95C ARG* 1.3 60.8 + - - +
96C VAL* 5.8 0.2 - - - -
107C VAL 3.4 6.7 - - - +
108C THR* 4.6 13.7 - - + -
178C LYS 4.0 0.7 - - - +
179C THR* 3.3 2.8 - - - -
180C THR* 2.9 43.2 + - + +
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Residues in contact with ARG 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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63C PRO* 3.1 26.5 + - - +
64C GLN* 2.9 28.4 + - - -
66C CH6 2.6 28.5 + - - +
70C LYS* 4.3 1.0 - - - +
93C TRP* 3.6 25.0 - - + -
94C GLU* 1.3 74.7 - - - +
96C VAL* 1.3 72.1 + - - +
97C MET* 4.0 13.4 - - + +
106C THR* 3.3 5.0 - - - -
107C VAL* 2.8 37.6 + - + +
148C GLU* 4.9 0.8 + - - -
161C ILE* 5.7 3.2 - - - +
177C VAL* 3.8 22.6 - - + +
178C LYS 3.4 4.5 - - - +
179C THR* 2.8 22.9 + - - +
181C TYR* 3.2 23.8 + - - -
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Residues in contact with VAL 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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94C GLU 5.8 0.4 - - - -
95C ARG* 1.3 80.5 - - - +
97C MET* 1.3 68.7 + - - +
98C ASN* 3.8 27.4 - - - +
104C VAL* 5.1 2.9 - - + -
105C VAL 3.5 4.5 - - - +
106C THR* 4.3 17.0 - - + -
176C GLU 3.8 1.0 - - - +
177C VAL* 3.4 4.0 - - - +
178C LYS* 3.0 37.6 + - + +
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Residues in contact with MET 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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60C ILE 4.6 2.9 - - - +
63C PRO* 4.6 6.3 - - + -
64C GLN* 3.4 29.2 - - - +
95C ARG* 4.0 14.4 - - + -
96C VAL* 1.3 77.6 - - - +
98C ASN* 1.3 62.9 + - - +
99C PHE* 3.8 17.7 - - + -
104C VAL* 3.4 7.3 - - - +
105C VAL* 2.7 51.4 + - + +
107C VAL* 5.2 0.2 - - + -
143C 4OO 2.9 40.2 - - - +
163C GLN* 5.0 2.5 - - + +
175C ALA* 4.9 1.1 - - + -
176C GLU 3.5 4.5 - - - -
177C VAL* 3.8 23.6 - - + -
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Residues in contact with ASN 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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96C VAL* 3.8 20.3 - - - +
97C MET* 1.3 71.2 - - - +
99C PHE* 1.3 65.0 + - - +
103C GLY 3.8 0.9 - - - -
104C VAL* 3.5 25.3 - - - +
175C ALA* 3.2 2.1 - - - -
176C GLU* 2.9 51.8 + - + +
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Residues in contact with PHE 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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60C ILE* 3.9 24.0 - - + -
97C MET* 3.8 30.5 - - + -
98C ASN* 1.3 78.8 - - - +
100C GLU* 1.3 67.0 + - - +
101C ASP* 3.2 3.6 - - - +
102C GLY* 3.1 14.0 + - - -
103C GLY 2.8 29.5 + - - +
105C VAL* 3.9 16.8 - - + -
129C PHE* 3.9 6.5 - + - -
143C 4OO 3.3 31.4 - - - -
165C LEU* 4.3 4.7 - - + -
173C TYR* 3.2 45.8 - + + +
174C ASP 3.6 4.7 - - - -
175C ALA* 3.8 10.8 - - + -
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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