Contacts of the strand formed by residues 130 - 138 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438I ILE* 4.4 7.6 - - + -
125L ASN* 3.1 4.2 + - - -
126L VAL* 2.8 42.0 + - + +
127L GLY* 3.3 17.8 + - - +
128L PRO* 3.3 15.8 - - + +
129L GLY* 1.3 83.6 - - - +
131L ASP* 1.3 57.7 + - - +
478L THR* 3.6 26.9 - - + -
479L GLN 3.4 14.8 - - - +
480L ARG* 3.8 32.1 - - + +
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Residues in contact with ASP 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423J ARG* 2.8 46.6 + - - +
133K TRP* 6.1 1.0 - - - -
135K GLU* 4.3 10.9 - - - +
122L HIS* 4.4 15.5 + - + +
123L SER 3.5 10.1 - - - +
124L ARG* 3.8 6.3 - - - -
125L ASN 3.2 17.3 + - - -
126L VAL* 4.4 1.1 - - - -
129L GLY 4.4 0.2 + - - -
130L ILE* 1.3 75.2 - - - +
132L SER* 1.3 61.7 + - - +
133L TRP* 4.7 4.5 - - + -
478L THR* 3.5 2.9 - - - +
479L GLN* 2.7 47.0 + - + +
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Residues in contact with SER 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443I PRO* 5.5 2.6 - - - +
444I VAL* 5.6 2.8 + - - +
447I HIS* 4.1 10.9 + - - -
122L HIS* 5.3 0.2 - - - -
123L SER* 2.8 37.4 + - - -
126L VAL* 3.7 24.0 - - - +
131L ASP* 1.3 77.2 - - - +
133L TRP* 1.3 62.8 + - - +
476L THR* 3.7 14.9 - - - +
477L VAL 3.1 17.1 + - - -
478L THR* 3.6 12.7 + - - -
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Residues in contact with TRP 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426I SER* 4.6 8.3 - - - -
436I ILE* 5.5 0.7 - - + -
447I HIS* 4.4 5.2 - - - -
122K HIS* 3.3 47.2 + + + +
131K ASP* 6.1 0.9 - - - -
479K GLN* 6.2 0.2 - - - -
121L GLU 3.2 11.0 - - - +
122L HIS* 3.7 33.7 - + - +
131L ASP* 4.7 3.8 - - + -
132L SER* 1.3 82.4 - - - +
134L SER* 1.3 59.3 + - - +
135L GLU* 3.5 21.1 + - + +
476L THR* 3.5 3.6 - - - +
477L VAL* 2.9 64.7 + - + +
479L GLN* 3.7 47.1 - - + -
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Residues in contact with SER 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447I HIS* 4.2 7.3 - - - -
122K HIS* 4.2 3.1 - - - +
120L GLY* 3.3 23.1 - - - -
121L GLU* 2.9 38.7 + - - +
133L TRP* 1.3 77.2 - - - +
135L GLU* 1.3 67.8 + - - +
136L PHE* 4.7 5.9 - - - -
474L ARG* 3.6 30.0 + - - -
475L LYS 3.3 10.3 - - - -
476L THR* 4.5 2.7 - - - +
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Residues in contact with GLU 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426I SER* 4.9 4.0 + - - +
427I ASP* 4.0 5.4 - - - +
122K HIS* 3.2 26.5 + - + -
124K ARG* 3.8 22.2 - - + +
131K ASP* 4.1 10.6 - - - +
118L LEU 5.8 0.4 - - - -
120L GLY* 5.0 1.6 - - - -
133L TRP* 3.5 19.8 + - + -
134L SER* 1.3 79.9 - - - +
136L PHE* 1.3 65.6 + - - +
137L GLN* 2.8 35.9 + - + -
473L LYS 3.6 0.5 - - - +
474L ARG* 3.7 2.8 - - - +
475L LYS* 2.8 40.2 + - + +
477L VAL* 5.4 6.3 - - + -
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Residues in contact with PHE 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K ARG* 6.0 1.0 - - - -
117L LEU 5.4 3.1 - - - -
118L LEU* 4.2 28.1 + - + +
119L LYS 3.8 23.8 - - - -
120L GLY* 4.2 10.8 - - - -
121L GLU* 5.5 4.7 - - + -
134L SER* 4.7 5.4 - - - -
135L GLU* 1.3 75.1 - - - +
137L GLN* 1.3 64.7 + - - +
138L PRO* 4.1 1.6 - - - +
165L CYS 5.3 0.3 - - - +
468L VAL* 5.3 2.9 - - + +
469L ARG* 3.5 47.1 - - - -
472L THR* 3.4 29.3 - - + +
473L LYS 3.5 3.6 - - - -
474L ARG* 3.9 40.6 - - + -
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Residues in contact with GLN 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427I ASP* 3.1 33.4 + - - +
452I TRP* 3.3 23.6 - - + -
124K ARG* 4.0 11.1 - - - +
57L ARG* 3.5 13.0 + - - +
135L GLU* 2.8 37.0 + - + +
136L PHE* 1.3 75.8 - - - +
138L PRO* 1.3 75.3 - - + +
472L THR* 3.3 4.3 - - - -
473L LYS* 2.9 31.6 + - - +
475L LYS* 3.0 31.6 + - + +
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Residues in contact with PRO 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124K ARG* 4.2 14.1 - - - +
53L PHE* 3.7 14.6 - - + -
57L ARG* 3.8 27.4 + - + +
64L ARG* 4.8 1.3 - - - +
136L PHE 4.5 0.9 - - - +
137L GLN* 1.3 92.8 - - + +
139L MET* 1.3 64.0 + - - +
165L CYS 3.3 21.5 - - - +
166L GLY* 3.3 34.1 - - - +
167L ASN* 3.7 2.2 - - - +
471L TYR 4.3 2.9 - - - +
473L LYS* 3.3 17.0 - - - -
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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