Contacts of the strand formed by residues 125 - 131 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ILE 3.6 0.2 - - - +
92G LEU* 3.4 6.4 - - - +
93G VAL* 2.9 41.1 + - + -
95G VAL* 3.8 19.3 - - + -
100G TYR* 3.4 45.8 - - + +
103G VAL* 4.1 2.9 - - + -
104G ALA* 3.8 16.2 - - + +
107G LEU* 4.0 25.4 - - - -
116G VAL* 4.0 8.7 - - + -
117G TYR 3.1 11.4 - - - +
118G GLU* 4.2 11.9 - - + -
119G THR* 3.8 2.5 - - - -
123G TYR* 4.6 1.0 - - - +
124G ASP* 1.3 86.3 + - - +
126G VAL* 1.3 67.5 + - - +
127G VAL* 4.1 1.3 - - + -
162H HIS* 4.4 2.7 - - + +
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Residues in contact with VAL 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G PHE* 3.8 31.2 - - + -
91G ILE 3.6 3.6 - - - +
92G LEU* 3.9 12.3 - - + -
116G VAL* 3.5 3.1 - - - -
117G TYR* 2.9 36.9 + - + +
119G THR* 3.8 14.7 + - + +
125G MET* 1.3 76.6 - - - +
127G VAL* 1.3 65.1 + - - +
128G LYS 4.9 0.4 - - - +
90H PHE* 4.1 30.7 - - + -
156H MET* 3.7 30.3 - - + -
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Residues in contact with VAL 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ALA 3.7 0.7 - - - +
90G PHE* 3.2 6.1 - - - -
91G ILE* 2.7 55.8 + - + +
93G VAL* 3.9 22.2 - - + -
107G LEU* 3.9 23.3 - - + -
113G ILE* 3.7 39.7 - - + -
115G GLU 3.4 3.4 - - - -
116G VAL* 4.3 10.5 - - + -
125G MET* 4.7 1.8 - - + -
126G VAL* 1.3 82.5 - - - +
128G LYS* 1.3 65.6 + - - +
129G ILE 4.0 0.2 + - - -
144G ILE* 5.6 0.4 - - + -
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Residues in contact with LYS 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LEU* 3.6 24.0 - - + -
89G ALA 3.5 6.1 - - - +
90G PHE* 3.6 32.5 - - + -
113G ILE* 3.5 4.3 - - - +
114G VAL* 2.9 49.1 + - + -
115G GLU* 2.8 49.2 + - + +
117G TYR* 6.0 0.4 - - + -
126G VAL* 4.2 1.0 - - - +
127G VAL* 1.3 72.1 - - - +
129G ILE* 1.3 61.9 + - - +
130G ARG* 4.7 6.8 - - - +
164G GLU* 4.5 2.8 + - - +
115H GLU* 2.8 26.6 + - - -
117H TYR* 3.2 15.2 + - - +
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Residues in contact with ILE 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G MET* 5.8 0.6 - - + +
88G LEU* 3.4 6.2 - - - +
89G ALA* 3.0 53.5 + - + +
91G ILE* 3.8 29.6 - - + -
112G GLU* 3.4 15.9 - - + +
113G ILE* 3.9 20.4 - - + -
127G VAL* 4.0 0.6 + - + -
128G LYS* 1.3 76.3 - - - +
130G ARG* 1.3 66.3 + - - +
131G THR* 4.0 13.9 - - + -
137G LEU* 3.9 10.3 - - + -
140G PHE* 3.7 38.4 - - + -
144G ILE* 4.6 0.2 - - + -
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Residues in contact with ARG 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G PRO* 3.5 32.8 - - - +
85G TYR* 3.7 19.0 + - + -
87G MET 3.4 8.9 + - - +
88G LEU* 3.7 32.2 - - + +
112G GLU* 2.9 38.0 + - - +
114G VAL* 4.7 16.9 - - + +
128G LYS* 4.7 6.9 - - - +
129G ILE* 1.3 76.9 - - - +
131G THR* 1.3 63.8 + - - +
164G GLU* 2.7 37.8 + - - +
117H TYR* 4.6 0.4 + - - -
168H LEU* 3.6 30.7 - - + +
169H PRO* 5.8 2.9 - - + -
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Residues in contact with THR 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G TYR* 3.5 9.8 - - - -
86G SER 3.6 3.3 + - - -
87G MET* 2.9 54.7 + - + +
129G ILE* 4.0 13.7 - - + -
130G ARG* 1.3 80.4 - - - +
132G LYS* 1.3 60.8 + - - +
133G ASN 2.9 13.6 + - - -
136G GLU* 3.5 13.5 - - - -
137G LEU* 3.6 17.2 - - + +
140G PHE* 3.7 30.1 - - + -
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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