Contacts of the strand formed by residues 130 - 138 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438J ILE* 4.2 10.3 - - + -
125K ASN* 3.1 5.0 + - - -
126K VAL* 2.8 41.8 + - + +
127K GLY* 2.8 20.0 + - - +
128K PRO* 3.6 13.0 - - + +
129K GLY* 1.3 83.8 - - - +
131K ASP* 1.3 62.1 + - - +
478K THR* 3.6 26.7 - - + -
479K GLN 3.5 12.1 - - - +
480K ARG* 3.8 32.5 - - + +
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Residues in contact with ASP 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I ARG* 2.9 46.7 + - - +
122K HIS* 4.3 15.6 + - + +
123K SER 3.7 9.2 - - - +
124K ARG* 3.5 5.0 - - - -
125K ASN 2.9 20.7 + - - -
126K VAL* 4.4 1.1 - - - -
129K GLY 4.3 0.4 + - - -
130K ILE* 1.3 74.3 - - - +
132K SER* 1.3 59.1 + - - +
133K TRP* 4.6 5.6 - - + -
478K THR* 3.5 2.8 - - - +
479K GLN* 2.8 48.1 + - - +
133L TRP* 6.1 0.9 - - - -
135L GLU* 4.1 11.0 - - - +
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Residues in contact with SER 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443J PRO* 5.5 2.3 - - - +
444J VAL* 5.6 2.7 - - - +
447J HIS* 4.1 9.8 + - - -
122K HIS* 4.7 0.4 - - - -
123K SER* 2.7 38.7 + - - +
126K VAL* 3.9 24.8 - - - +
131K ASP* 1.3 76.0 - - - +
133K TRP* 1.3 64.9 + - - +
476K THR* 3.7 13.7 - - - +
477K VAL 2.9 17.7 + - - -
478K THR* 3.4 14.4 + - - -
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Residues in contact with TRP 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426J SER* 4.8 7.9 - - - -
436J ILE* 5.5 0.4 - - + -
447J HIS* 4.3 2.5 - - - -
121K GLU 3.1 12.8 - - - +
122K HIS* 3.7 30.5 - + - +
131K ASP* 4.7 4.0 - - + -
132K SER* 1.3 85.2 + - - +
134K SER* 1.3 61.2 + - - +
135K GLU* 3.5 21.2 + - + +
475K LYS 3.8 0.5 - - - +
476K THR* 3.5 6.3 - - - -
477K VAL* 2.9 66.3 + - + +
479K GLN* 3.8 46.0 - - + -
122L HIS* 3.4 46.2 + + + +
131L ASP* 6.1 0.7 - - - -
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Residues in contact with SER 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447J HIS* 4.2 7.8 - - - -
120K GLY* 3.3 19.4 - - - -
121K GLU* 2.8 40.6 + - - +
133K TRP* 1.3 78.0 - - - +
135K GLU* 1.3 66.8 + - - +
136K PHE* 4.5 6.9 - - - -
474K ARG* 3.5 32.0 + - - -
475K LYS 3.2 8.3 - - - -
476K THR* 4.4 2.7 - - - +
122L HIS* 4.2 3.5 - - - +
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Residues in contact with GLU 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423J ARG* 5.5 0.2 + - - -
426J SER* 5.3 3.6 + - - -
427J ASP* 3.9 7.8 - - - +
118K LEU 6.0 0.2 - - - -
120K GLY* 5.0 1.3 - - - -
133K TRP* 3.5 28.3 + - + +
134K SER* 1.3 79.2 - - - +
136K PHE* 1.3 63.5 + - - +
137K GLN* 2.7 42.4 + - + +
473K LYS 3.4 2.1 - - - +
474K ARG* 3.7 1.0 - - - -
475K LYS* 2.7 41.4 + - + +
477K VAL* 5.1 7.5 - - + +
122L HIS* 3.5 17.3 + - + -
124L ARG* 3.5 25.4 - - + +
131L ASP* 4.3 9.0 - - - +
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Residues in contact with PHE 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K LEU 5.0 5.2 - - - -
118K LEU* 4.2 27.3 + - + +
119K LYS 3.5 25.4 - - - -
120K GLY* 4.2 7.4 - - - -
121K GLU* 5.7 5.4 - - + -
134K SER* 4.5 7.2 - - - -
135K GLU* 1.3 74.5 - - - +
137K GLN* 1.3 64.8 + - - +
138K PRO* 4.1 0.9 - - - +
165K CYS 5.3 0.9 - - - +
468K VAL* 5.7 3.4 - - + -
469K ARG* 3.8 37.9 - - - -
472K THR* 3.4 28.8 - - + +
473K LYS 3.6 3.6 - - - -
474K ARG* 3.8 48.5 - - + -
124L ARG* 6.1 1.1 - - - -
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Residues in contact with GLN 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427J ASP* 3.2 30.4 + - - +
452J TRP* 3.3 19.2 - - + -
57K ARG* 3.5 13.3 + - - +
135K GLU* 2.7 38.4 + - + +
136K PHE* 1.3 74.8 - - - +
138K PRO* 1.3 75.6 - - + +
472K THR* 3.2 4.8 - - - -
473K LYS* 2.9 34.8 + - - +
475K LYS* 3.3 34.0 + - + +
124L ARG* 4.2 9.4 - - - +
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Residues in contact with PRO 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K PHE* 3.8 13.5 - - + -
57K ARG* 3.8 29.5 + - + +
64K ARG* 4.9 2.0 - - - +
136K PHE 4.6 0.7 - - - +
137K GLN* 1.3 90.4 - - + +
139K MET* 1.3 63.9 + - - +
165K CYS 3.4 22.6 - - - +
166K GLY* 3.4 31.4 - - - +
167K ASN* 3.7 3.8 - - - +
471K TYR 4.3 3.1 - - - +
473K LYS* 3.2 17.7 - - - -
124L ARG* 4.0 16.2 - - - +
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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