Contacts of the strand formed by residues 87 - 95 (chain H) in PDB entry 2ZNZ
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 MET 87 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H TYR* 3.4 2.4 - - - +
86H SER* 1.3 79.7 + - - +
88H LEU* 1.3 72.7 + - - +
89H ALA* 4.5 2.5 - - + +
129H ILE* 5.4 0.9 - - + +
130H ARG* 3.3 9.9 + - - +
131H THR* 3.0 54.4 + - + +
133H ASN* 4.2 8.5 - - - +
134H SER* 3.6 35.7 - - - +
137H LEU* 4.1 16.6 - - + -
157H ILE* 3.9 37.9 - - + -
158H VAL 5.8 0.4 - - - +
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Residues in contact with LEU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G TYR* 3.5 36.8 - - + -
86H SER 4.3 1.0 + - - -
87H MET* 1.3 80.4 - - - +
89H ALA* 1.3 70.0 + - - +
90H PHE* 5.5 0.7 - - + -
128H LYS* 3.6 35.0 - - + -
129H ILE 3.6 7.4 - - - +
130H ARG* 3.8 31.4 - - + +
157H ILE 3.9 0.2 - - - -
158H VAL* 2.9 46.9 + - + +
161H THR* 4.1 5.4 - - - +
164H GLU* 3.9 5.6 - - - +
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Residues in contact with ALA 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H MET* 4.5 2.5 - - + -
88H LEU* 1.3 78.8 - - - +
90H PHE* 1.3 65.5 + - - +
128H LYS* 3.6 5.9 - - - +
129H ILE* 3.0 50.3 + - + +
137H LEU* 4.2 14.1 - - + -
155H THR* 3.9 20.9 - - + -
156H MET 3.4 10.8 - - - +
157H ILE* 4.3 3.8 - - + -
158H VAL* 4.4 1.1 - - - +
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Residues in contact with PHE 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G PHE* 3.8 25.6 - + - -
117G TYR* 3.5 42.2 - + - -
119G THR* 4.6 2.0 - - + -
126G VAL* 4.1 25.8 - - + -
88H LEU* 5.4 0.9 - - + -
89H ALA* 1.3 73.0 - - - +
91H ILE* 1.3 60.6 + - - +
92H LEU* 4.0 3.3 - - + +
115H GLU* 4.8 0.2 - - - -
126H VAL* 3.8 24.2 - - + -
127H VAL 3.3 8.1 - - - -
128H LYS* 3.6 32.3 - - + -
154H HIS 3.8 1.0 - - - +
155H THR* 3.4 2.3 - - - +
156H MET* 2.7 56.8 + - + +
158H VAL* 4.0 19.5 - - + -
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Residues in contact with ILE 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H PHE* 1.3 75.4 - - - +
92H LEU* 1.3 66.2 + - - +
93H VAL* 3.8 12.6 + - + +
125H MET 3.6 3.5 - - - +
126H VAL* 3.6 0.6 - - - -
127H VAL* 2.8 45.4 + - + +
129H ILE* 3.6 37.0 - - + -
137H LEU* 4.4 3.1 - - + -
140H PHE* 5.8 0.2 - - + -
141H LEU* 3.7 19.5 - - + -
144H ILE* 3.8 21.1 - - + -
153H THR* 3.8 29.4 - - + -
154H HIS 3.7 2.2 - - - +
155H THR* 3.7 19.3 - - + +
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Residues in contact with LEU 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G LEU* 5.7 2.2 - - + -
156G MET* 4.1 25.6 - - + -
90H PHE* 5.3 3.6 - - + +
91H ILE* 1.3 73.9 - - - +
93H VAL* 1.3 58.5 + - - +
119H THR* 5.8 0.2 - - - +
123H TYR* 3.7 34.8 - - + -
125H MET 3.4 4.3 - - - +
126H VAL* 3.6 31.0 - - + -
153H THR* 3.1 7.6 - - - -
154H HIS* 2.8 54.5 + - + +
156H MET* 4.4 24.0 - - - -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H ILE* 3.9 24.2 - - + +
92H LEU* 1.3 78.0 - - - +
94H LYS* 1.3 61.6 - - - +
95H VAL* 4.0 10.9 - - + +
103H VAL* 4.7 1.8 - - + -
107H LEU* 4.3 13.7 - - + -
123H TYR* 3.8 3.5 - - - -
124H ASP* 3.0 21.7 + - - +
125H MET* 3.0 34.4 + - + +
127H VAL* 4.5 4.7 - - + -
144H ILE* 4.5 6.5 - - + -
150H VAL* 3.8 37.9 - - + -
152H GLY 3.6 3.6 - - - +
153H THR* 4.3 5.4 - - + -
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Residues in contact with LYS 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H VAL* 1.3 71.2 - - - +
95H VAL* 1.3 58.5 + - - +
122H ASP* 2.7 46.8 + - - +
123H TYR* 3.6 23.1 - - + -
124H ASP* 3.5 9.9 + - - +
150H VAL* 3.5 5.4 - - - +
151H GLU* 2.7 53.6 + - + +
152H GLY* 2.8 23.6 + - - +
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Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H VAL* 4.0 10.3 - - + +
94H LYS* 1.3 78.4 - - - +
96H LYS* 1.3 79.4 + - - +
97H ALA* 3.3 2.1 + - - -
99H LYS* 3.7 26.9 - - + +
100H TYR* 3.8 19.1 - - + +
103H VAL* 3.8 24.2 - - + -
124H ASP* 2.7 19.7 + - + +
125H MET* 3.6 30.1 - - + -
149H GLY 3.3 9.2 - - - +
150H VAL* 5.0 0.4 - - + -
151H GLU* 4.2 8.3 - - - +
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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