Contacts of the strand formed by residues 90 - 96 (chain A) in PDB entry 2Z7S
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 LEU 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.3 32.8 - - + -
78A LEU* 4.2 6.5 - - + -
79A VAL 3.4 4.0 - - - +
80A ARG* 4.0 20.4 - - - +
88A GLY 3.5 3.1 + - - +
89A HIS* 1.3 75.3 - - - +
91A TYR* 1.3 70.4 + - - +
143A PHE* 4.1 32.9 + - + +
145A ARG* 3.9 30.9 + - - +
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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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62A PHE* 4.3 3.6 - + - -
78A LEU* 3.7 5.2 - - - +
79A VAL* 2.8 39.7 + - + +
81A LYS* 3.8 16.6 - - + -
86A ASP* 2.5 36.2 + - - +
89A HIS* 3.5 37.3 - + + +
90A LEU* 1.3 78.0 - - - +
92A ALA* 1.3 60.0 + - - +
128A HIS* 3.5 39.4 + + + -
129A TYR* 4.0 10.8 - + - -
140A ILE* 3.5 25.8 - - + -
141A LEU 3.5 16.2 - - - +
142A ASP* 4.9 1.8 - - - -
143A PHE* 3.8 9.9 - - - -
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Residues in contact with ALA 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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1A P01 3.6 33.7 - - + +
68A LEU* 4.8 3.6 - - + -
76A VAL* 4.2 4.9 - - + -
77A PHE 3.3 6.7 - - - +
78A LEU* 4.8 0.9 - - - +
91A TYR* 1.3 74.1 - - - +
93A MET* 1.3 60.1 + - - +
94A LYS 4.1 0.3 + - - -
139A LEU 3.6 1.4 - - - +
140A ILE* 3.7 1.2 - - - -
141A LEU* 2.8 35.4 + - - +
142A ASP 3.4 20.0 - - - +
143A PHE* 3.9 6.1 - - + +
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Residues in contact with MET 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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59A PRO* 6.0 2.9 - - - +
62A PHE* 5.0 8.1 - - - -
64A LEU* 3.6 31.2 - - + -
75A LYS 3.4 1.7 - - - +
76A VAL* 3.2 6.6 - - - -
77A PHE* 2.7 62.7 + - + +
79A VAL* 3.6 26.0 - - + -
91A TYR 3.9 0.6 + - - -
92A ALA* 1.3 73.9 - - - +
94A LYS* 1.3 67.7 + - - +
95A VAL* 4.1 9.9 - - + -
131A PHE* 5.7 0.2 - - - -
138A TYR* 3.7 26.2 - - + -
139A LEU 3.4 4.3 - - - +
140A ILE* 3.7 21.1 - - + -
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Residues in contact with LYS 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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1A P01 5.0 6.1 - - + +
73A PHE* 3.2 48.4 - - + +
75A LYS 3.5 3.6 - - - +
76A VAL* 4.0 23.6 - - + -
92A ALA 4.1 0.4 + - - -
93A MET* 1.3 73.6 - - - +
95A VAL* 1.3 63.0 + - - +
96A LEU* 4.7 6.3 - - + -
137A LEU 3.4 3.6 - - - +
138A TYR* 3.5 2.4 - - - -
139A LEU* 2.9 57.5 + - + +
141A LEU* 4.3 16.8 - - + +
204A THR* 4.9 3.2 + - - -
205A ASP* 2.5 34.4 + - - +
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Residues in contact with VAL 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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74A GLY* 3.7 13.3 - - - -
75A LYS* 3.4 13.5 + - + +
77A PHE* 3.6 34.3 - - + -
93A MET* 4.1 14.4 - - + -
94A LYS* 1.3 78.2 - - - +
96A LEU* 1.3 69.5 + - - +
97A LYS* 4.5 6.1 + - + +
136A LYS* 5.4 11.9 - - + -
137A LEU 3.6 4.0 - - - +
138A TYR* 4.2 21.3 - - + +
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Residues in contact with LEU 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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73A PHE* 2.8 40.4 - - + +
74A GLY* 4.3 1.8 - - - -
94A LYS* 4.7 9.6 - - + +
95A VAL* 1.3 83.7 - - - +
97A LYS* 1.3 64.7 + - - +
135A GLY 3.3 0.5 - - - +
136A LYS* 2.9 8.1 - - - -
137A LEU* 2.6 52.0 + - + +
139A LEU* 4.5 25.4 - - + -
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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