Contacts of the strand formed by residues 125 - 131 (chain A) 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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.5 6.6 - - - +
93A VAL* 3.0 39.6 + - + -
95A VAL* 4.0 17.5 - - + -
100A TYR* 3.5 43.3 - - + +
103A VAL* 4.1 4.7 - - + -
104A ALA* 3.8 17.5 - - + +
107A LEU* 3.9 24.9 - - - -
116A VAL* 4.1 7.2 - - + -
117A TYR 3.0 12.8 - - - +
118A GLU* 4.2 12.6 - - + -
119A THR* 3.8 2.9 + - - -
123A TYR* 3.8 0.9 - - - +
124A ASP* 1.3 83.2 + - + +
126A VAL* 1.3 67.8 + - - +
127A VAL* 4.1 2.5 - - + -
162B HIS* 4.4 2.9 - - + +
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Residues in contact with VAL 126 (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 PHE* 3.7 33.2 - - + -
91A ILE 3.6 3.4 - - - +
92A LEU* 3.9 9.4 - - + -
116A VAL* 3.5 2.8 - - - -
117A TYR* 3.0 35.7 + - + -
119A THR* 3.8 12.5 + - + +
125A MET* 1.3 75.4 - - - +
127A VAL* 1.3 64.0 + - - +
128A LYS 4.9 0.4 - - - +
90B PHE* 4.1 30.1 - - + -
156B MET* 3.2 35.2 - - + -
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Residues in contact with VAL 127 (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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89A ALA 3.7 0.3 - - - +
90A PHE* 3.2 5.6 - - - -
91A ILE* 2.7 57.0 + - + +
93A VAL* 3.9 16.2 - - + -
107A LEU* 3.9 28.9 - - + -
113A ILE* 3.6 41.7 - - + -
115A GLU 3.3 3.1 - - - -
116A VAL* 4.3 11.0 - - + -
125A MET* 4.7 2.2 - - + -
126A VAL* 1.3 82.1 - - - +
128A LYS* 1.3 64.3 + - - +
129A ILE 3.9 0.3 + - - -
144A ILE* 5.6 0.2 - - + -
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Residues in contact with LYS 128 (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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88A LEU* 3.6 24.5 - - + -
89A ALA 3.5 5.6 - - - +
90A PHE* 3.7 29.8 - - + -
113A ILE* 3.6 3.6 - - - -
114A VAL* 3.0 48.3 + - + -
115A GLU* 3.0 46.9 + - + +
117A TYR* 6.0 0.6 - - + -
126A VAL* 4.2 1.4 + - - +
127A VAL* 1.3 72.2 - - - +
129A ILE* 1.3 62.3 + - - +
130A ARG* 4.6 7.4 - - - +
164A GLU* 4.5 3.0 + - - +
115B GLU* 2.9 26.0 + - - -
117B TYR* 3.1 21.1 + - - -
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Residues in contact with ILE 129 (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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87A MET* 5.7 0.6 - - + +
88A LEU* 3.6 5.6 - - - +
89A ALA* 2.9 44.4 + - + +
91A ILE* 3.7 30.5 - - + -
112A GLU* 3.5 17.0 - - + +
113A ILE* 3.9 20.6 - - + -
127A VAL* 3.9 0.6 + - + -
128A LYS* 1.3 75.4 - - - +
130A ARG* 1.3 66.4 + - - +
131A THR* 4.0 14.1 - - + -
137A LEU* 3.8 18.4 - - + -
140A PHE* 3.8 36.6 - - + -
144A ILE* 4.6 0.4 - - + -
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Residues in contact with ARG 130 (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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80A PRO* 3.5 32.1 - - - +
85A TYR* 3.6 19.9 + - + -
87A MET 3.4 9.1 + - - +
88A LEU* 3.8 33.8 - - + +
112A GLU* 3.0 36.5 + - - +
114A VAL* 4.6 20.0 - - + +
128A LYS* 4.6 7.3 - - - +
129A ILE* 1.3 76.6 - - - +
131A THR* 1.3 64.2 + - - +
164A GLU* 2.6 35.8 + - - -
117B TYR* 4.5 1.0 + - - -
168B LEU* 3.6 29.7 - - + +
169B PRO* 5.7 2.5 - - + -
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Residues in contact with THR 131 (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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85A TYR* 3.5 9.0 - - - -
86A SER 3.6 3.1 + - - -
87A MET* 2.9 47.7 + - + +
129A ILE* 4.0 15.0 - - + -
130A ARG* 1.3 79.9 - - - +
132A LYS* 1.3 61.7 + - - +
133A ASN 2.8 21.7 + - - -
136A GLU* 3.4 17.0 - - + +
137A LEU* 3.6 17.4 - - + +
140A PHE* 3.8 28.7 - - + -
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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