Contacts of the strand formed by residues 130 - 138 (chain G) in PDB entry 4ZZ7
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 ILE 130 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125G ASN* 3.0 5.0 + - - -
126G VAL* 2.7 42.2 + - + +
127G GLY* 3.2 19.7 + - - +
128G PRO* 3.5 15.7 - - + +
129G GLY* 1.3 82.5 - - - +
131G ASP* 1.3 57.9 + - - +
478G THR* 3.7 26.5 - - + -
479G GLN 3.5 15.9 - - - +
480G ARG* 4.0 26.2 - - + +
438H ILE* 4.6 9.2 - - + -
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Residues in contact with ASP 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E ARG* 2.9 47.8 + - - +
133F TRP* 5.8 2.4 + - - -
135F GLU* 4.5 5.7 - - - +
122G HIS* 4.4 19.5 + - + +
123G SER 3.5 8.1 - - - +
124G ARG* 3.6 6.9 - - - +
125G ASN 3.2 17.8 + - - -
126G VAL* 4.5 0.9 - - - -
129G GLY 4.2 0.2 - - - -
130G ILE* 1.3 73.1 - - - +
132G SER* 1.3 61.2 + - - +
133G TRP* 4.7 2.7 - - + -
478G THR* 3.7 2.6 - - - +
479G GLN* 2.8 46.7 + - + +
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Residues in contact with SER 132 (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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122G HIS* 4.5 0.5 + - - -
123G SER* 2.8 40.1 + - - +
126G VAL* 3.8 24.8 - - - +
131G ASP* 1.3 75.4 - - - +
133G TRP* 1.3 61.6 + - - +
476G THR* 3.9 13.5 - - - +
477G VAL 2.7 20.8 + - - -
478G THR* 3.2 14.9 + - - -
443H PRO* 5.5 2.3 - - - +
444H VAL* 5.5 2.9 - - - +
447H HIS* 4.8 7.1 - - - -
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Residues in contact with TRP 133 (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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122F HIS* 3.3 45.4 + + + +
131F ASP* 5.9 2.5 - - - -
133F TRP* 6.5 1.6 - + - -
121G GLU 3.1 15.3 - - - +
122G HIS* 3.7 29.6 - + - +
131G ASP* 4.6 4.7 - - + -
132G SER* 1.3 80.9 + - - +
134G SER* 1.3 59.0 + - - +
135G GLU* 3.4 24.8 + - + +
475G LYS 3.9 0.3 - - - +
476G THR* 4.5 2.7 - - - -
477G VAL* 2.9 64.2 + - + +
479G GLN* 3.9 43.7 - - + -
426H SER* 4.8 8.3 - - - -
436H ILE* 5.5 0.4 - - + -
447H HIS* 4.4 5.2 - - - -
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Residues in contact with SER 134 (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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122F HIS* 4.4 2.8 - - - +
120G GLY* 3.4 19.3 - - - -
121G GLU* 2.9 38.3 + - - +
133G TRP* 1.3 78.4 - - - +
135G GLU* 1.3 64.6 + - - +
136G PHE* 4.5 7.9 - - - -
474G ARG* 3.5 33.2 + - - -
475G LYS 3.3 8.1 - - - -
476G THR* 4.5 2.9 - - - +
447H HIS* 4.1 10.1 - - - -
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Residues in contact with GLU 135 (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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122F HIS* 3.2 24.6 + - + -
124F ARG* 3.6 26.4 - - + +
131F ASP* 4.5 7.1 - - - +
120G GLY* 5.0 2.2 - - - -
133G TRP* 3.4 28.0 + - + +
134G SER* 1.3 72.1 - - - +
136G PHE* 1.3 64.1 + - - +
137G GLN* 3.0 35.6 + - + +
474G ARG* 3.7 0.7 - - - -
475G LYS* 2.8 41.2 + - + +
477G VAL* 5.2 5.8 - - + -
423H ARG* 5.5 0.9 + - - -
426H SER* 4.8 3.5 + - - +
427H ASP* 4.3 3.7 - - - +
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Residues in contact with PHE 136 (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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124F ARG* 5.8 2.5 - - - -
117G LEU 5.4 2.9 - - - -
118G LEU* 4.1 28.5 + - + +
119G LYS 3.7 25.1 - - - -
120G GLY* 4.2 11.0 - - - -
121G GLU* 5.9 4.7 - - + -
134G SER* 4.5 7.4 - - - -
135G GLU* 1.3 71.0 - - - +
137G GLN* 1.3 63.2 + - - +
138G PRO* 4.9 0.5 - - - +
165G CYS 5.5 0.2 - - - +
468G VAL* 5.7 3.4 - - + -
469G ARG* 3.7 45.5 - - - -
472G THR* 3.4 26.7 - - + +
473G LYS 3.8 2.9 - - - -
474G ARG* 3.8 49.1 - - + -
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Residues in contact with GLN 137 (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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124F ARG* 3.9 10.1 - - - +
57G ARG* 3.5 12.8 + - - +
135G GLU* 3.0 38.6 + - + +
136G PHE* 1.3 75.9 - - - +
138G PRO* 1.3 73.4 - - + +
472G THR* 3.2 7.7 - - - -
473G LYS 2.9 33.5 + - - +
475G LYS* 3.3 33.4 + - + +
427H ASP* 3.0 35.2 + - - +
430H GLN* 5.2 0.3 + - - -
452H TRP* 3.3 15.4 - - + -
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Residues in contact with PRO 138 (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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124F ARG* 4.1 15.7 - - - +
53G PHE* 3.8 12.0 - - + -
57G ARG* 3.8 31.5 + - + +
64G ARG* 4.9 1.8 - - - +
136G PHE 4.9 0.2 - - - +
137G GLN* 1.3 91.1 - - + +
139G MET* 1.3 60.9 + - - +
165G CYS 3.5 18.8 - - - +
166G GLY* 3.2 34.1 - - - +
167G ASN* 3.7 3.1 - - - +
471G TYR 4.4 3.6 - - - +
473G LYS* 3.1 20.8 - - - -
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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