Contacts of the strand formed by residues 130 - 138 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ASN* 3.1 4.1 + - - -
126A VAL* 2.8 38.6 + - + +
127A GLY* 3.0 18.6 + - - +
128A PRO* 3.5 13.2 - - + +
129A GLY* 1.3 83.6 - - - +
131A ASP* 1.3 60.9 + - - +
478A THR* 3.5 28.3 - - + -
479A GLN 3.5 16.2 - - - +
480A ARG* 3.9 26.5 - - + +
438B ILE* 4.1 10.1 - - + -
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Residues in contact with ASP 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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122A HIS* 4.5 18.1 + - + +
123A SER 3.5 9.9 - - - +
124A ARG* 3.6 6.4 - - - -
125A ASN* 3.0 20.7 + - - +
126A VAL* 4.7 0.2 - - - -
129A GLY 4.3 0.2 - - - -
130A ILE* 1.3 75.3 - - - +
132A SER* 1.3 62.7 + - - +
133A TRP* 4.6 9.2 - - + -
478A THR* 3.5 2.3 - - - +
479A GLN* 2.8 39.1 + - + +
423C ARG* 2.9 46.5 + - - +
135D GLU* 4.6 5.6 - - - +
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Residues in contact with SER 132 (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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122A HIS* 4.4 0.3 - - - -
123A SER* 2.7 39.6 + - - +
126A VAL* 3.9 22.9 - - - +
131A ASP* 1.3 75.4 - - - +
133A TRP* 1.3 62.0 + - - +
476A THR* 3.5 13.5 - - - +
477A VAL 2.6 20.5 + - - -
478A THR* 3.2 17.8 + - - -
443B PRO* 5.5 2.3 - - - +
444B VAL* 5.8 2.0 - - - -
447B HIS* 4.7 9.1 - - - -
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Residues in contact with TRP 133 (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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121A GLU 3.2 12.1 - - - +
122A HIS* 3.7 29.2 - + - +
131A ASP* 4.6 4.9 - - + -
132A SER* 1.3 84.6 + - - +
134A SER* 1.3 59.4 + - - +
135A GLU* 3.4 22.3 + - + +
475A LYS 3.8 0.3 - - - +
476A THR* 3.6 5.8 - - - -
477A VAL* 2.9 67.5 + - + +
479A GLN* 3.5 47.1 - - + -
426B SER* 4.8 8.1 - - - -
436B ILE* 5.3 0.2 - - + -
447B HIS* 4.4 2.7 - - - -
122D HIS* 3.3 47.4 + + + +
131D ASP* 6.1 0.4 - - - -
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Residues in contact with SER 134 (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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120A GLY* 3.5 18.6 - - - -
121A GLU* 2.8 41.2 + - - +
133A TRP* 1.3 78.6 - - - +
135A GLU* 1.3 68.7 + - - +
136A PHE* 4.1 9.8 - - - -
474A ARG* 3.5 31.1 + - - -
475A LYS 3.2 8.1 - - - -
476A THR* 4.5 2.9 - - - +
447B HIS* 4.2 7.3 - - - -
122D HIS* 4.1 4.3 - - - +
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Residues in contact with GLU 135 (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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120A GLY* 5.0 1.8 - - - -
133A TRP* 3.4 21.1 + - + +
134A SER* 1.3 80.3 - - - +
136A PHE* 1.3 63.8 + - - +
137A GLN* 2.7 42.1 + - + +
473A LYS 3.4 2.3 - - - +
474A ARG* 3.4 3.1 - - - +
475A LYS* 2.7 40.5 + - + +
477A VAL* 5.1 8.0 - - + +
426B SER* 5.7 2.1 + - - -
427B ASP* 3.9 8.5 - - - +
122D HIS* 3.3 24.0 + - + -
124D ARG* 3.7 21.5 - - + +
131D ASP* 4.4 9.4 - - - +
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Residues in contact with PHE 136 (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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117A LEU 5.5 2.0 - - - -
118A LEU* 4.0 29.7 + - + +
119A LYS 3.7 24.9 - - - -
120A GLY* 3.9 13.7 - - - -
121A GLU* 5.7 3.8 - - + -
134A SER* 4.1 8.7 - - - -
135A GLU* 1.3 75.1 - - - +
137A GLN* 1.3 63.8 + - - +
138A PRO* 4.2 0.7 - - - +
165A CYS 5.1 1.0 - - - +
468A VAL* 5.6 4.0 - - + -
469A ARG* 3.7 45.1 - - - -
472A THR* 3.4 27.8 - - + +
473A LYS 3.5 3.1 - - - -
474A ARG* 3.8 42.6 - - + -
124D ARG* 5.9 1.6 - - - +
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Residues in contact with GLN 137 (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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57A ARG* 3.3 18.9 + - - +
135A GLU* 2.7 38.0 + - + +
136A PHE* 1.3 76.1 - - - +
138A PRO* 1.3 72.7 - - + +
472A THR* 3.2 5.7 - - - -
473A LYS* 2.8 35.8 + - - +
475A LYS* 3.2 36.0 + - + +
427B ASP* 3.2 26.3 + - - +
452B TRP* 3.4 14.6 - - + -
124D ARG* 4.1 10.9 - - - +
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Residues in contact with PRO 138 (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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53A PHE* 3.9 12.0 - - + -
57A ARG* 3.9 31.7 + - + +
64A ARG* 5.1 1.3 - - - +
136A PHE 4.7 0.2 - - - +
137A GLN* 1.3 91.8 - - + +
139A MET* 1.3 63.6 + - - +
165A CYS 3.3 24.0 - - - +
166A GLY* 3.4 31.4 - - - +
167A ASN* 3.7 4.3 - - - +
471A TYR 4.4 2.9 - - - +
473A LYS* 3.2 19.3 - - - -
124D ARG* 4.2 11.7 - - - +
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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