Contacts of the strand formed by residues 132 - 137 (chain C) in PDB entry 4ERQ
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 VAL 132 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER* 4.1 5.9 + - - -
105C ALA* 3.5 33.8 - - + +
106C SER 3.1 19.7 + - - +
107C ASP* 4.5 0.3 + - - +
109C LYS* 3.5 34.5 - - - +
110C THR 3.7 8.7 - - - +
111C LEU* 3.7 23.8 - - + -
128C HIS* 3.7 23.6 - - + -
131C TYR* 1.3 74.5 - - - +
133C PHE* 1.3 61.4 + - - +
134C CYS 4.2 0.7 - - - +
146C SER* 4.1 4.0 - - - -
147C GLY 3.7 11.9 - - - +
148C SER* 4.2 0.9 - - - -
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Residues in contact with PHE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER* 3.5 10.3 - - - -
92C ASP* 3.4 8.1 - - - +
105C ALA* 4.1 3.8 - - - -
131C TYR 3.8 0.2 + - - -
132C VAL* 1.3 73.7 - - - +
134C CYS* 1.3 58.8 + - - +
147C GLY 2.9 9.3 + - - +
148C SER* 4.6 1.6 - - - -
149C PHE* 3.7 33.7 - + + -
174C VAL 3.7 13.2 - - - +
175C SER* 3.3 36.3 - - - -
191C TYR* 4.5 4.7 - + - -
261C CYS* 3.6 39.5 - - + -
5339F ALA* 3.8 17.0 - - + -
5340F ARG* 2.9 64.3 + - + -
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Residues in contact with CYS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASP* 3.4 13.0 - - - +
105C ALA* 4.0 1.7 - - - +
132C VAL* 3.8 2.6 - - - +
133C PHE* 1.3 78.7 - - - +
135C CYS* 1.3 66.0 - - - +
146C SER* 3.3 4.7 - - - -
147C GLY* 3.0 49.1 + - - +
174C VAL* 3.7 10.5 - - - -
175C SER 3.7 11.4 - - - +
176C ALA* 3.5 39.3 - - - -
177C VAL* 3.8 6.1 - - + +
5340F ARG* 4.0 2.9 - - - +
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Residues in contact with CYS 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LYS* 4.6 1.0 + - - -
92C ASP* 3.1 29.0 + - - +
93C VAL* 4.1 4.5 - - - -
94C ALA* 3.7 4.9 - - - +
103C VAL* 3.6 33.4 - - + -
104C SER 4.1 0.4 - - - -
105C ALA* 3.9 22.0 - - - -
111C LEU* 3.6 21.5 - - + -
134C CYS* 1.3 77.4 - - - +
136C ASN* 1.3 78.5 + - - +
144C ILE* 4.8 0.2 - - + -
145C VAL 3.2 10.8 - - - +
177C VAL* 3.9 3.2 - - - +
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Residues in contact with ASN 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LYS* 4.7 7.5 + - - +
94C ALA* 3.7 16.9 - - - +
103C VAL* 4.6 0.8 - - - +
135C CYS* 1.3 81.2 + - - +
137C PHE* 1.3 71.4 + - - +
144C ILE* 3.4 5.7 - - - +
145C VAL* 2.9 41.0 + - + +
177C VAL 2.8 26.7 + - - +
178C HIS* 3.5 27.1 - - + +
179C PHE* 4.8 1.1 - - + +
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Residues in contact with PHE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ALA* 3.6 10.0 - - - +
95C TRP 3.3 24.5 + - - +
96C SER* 3.6 20.0 - - - -
97C SER 5.1 0.2 - - - +
101C LEU* 4.0 27.1 - - + -
102C LEU 4.0 4.0 - - - -
103C VAL* 3.5 30.7 - - + -
113C ILE* 4.7 2.9 - - + -
136C ASN* 1.3 82.1 + - - +
138C ASN* 1.3 69.8 + - - +
139C PRO* 4.7 0.3 - - - +
141C SER* 3.8 24.5 - - - +
143C LEU 3.4 9.9 - - - -
144C ILE* 3.7 30.3 - - + +
158C VAL* 3.8 11.2 - - + -
178C HIS* 6.2 0.2 - - - -
179C PHE* 3.5 10.7 + - - +
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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