Contacts of the strand formed by residues 128 - 133 (chain F) in PDB entry 4CQM
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 GLY 128 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ASN* 3.2 15.5 - - - -
122F MET* 4.0 12.6 - - - -
127F GLY* 1.3 73.3 - - - -
129F SER* 1.3 61.2 + - - -
170F LYS 3.1 8.0 + - - +
171F ILE* 3.2 9.0 - - - +
172F ARG* 3.0 25.6 + - - +
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Residues in contact with SER 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ASN 2.8 8.9 + - - -
79F PHE* 3.5 27.7 - - - -
80F LEU 3.1 23.2 + - - +
122F MET* 4.4 1.8 - - - -
128F GLY* 1.3 74.6 - - - -
130F ILE* 1.3 66.6 + - - +
131F VAL* 5.3 5.1 - - - +
172F ARG* 3.3 42.9 + - - -
174F ASN* 5.5 0.5 + - - -
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Residues in contact with ILE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LEU* 3.6 35.7 - - + +
115F CYS* 3.8 30.5 - - + -
118F ALA* 4.6 2.9 - - + -
119F MET* 3.8 29.8 - - + -
122F MET* 4.1 17.0 - - - -
129F SER* 1.3 81.4 + - - +
131F VAL* 1.3 71.9 + - - +
132F ASN* 4.2 8.7 - - - +
171F ILE* 4.7 1.3 - - + -
172F ARG 2.6 16.3 + - - +
173F VAL* 3.5 16.2 - - + -
174F ASN* 2.9 27.5 + - - +
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Residues in contact with VAL 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LEU 3.0 12.5 + - - +
81F VAL* 3.6 13.8 - - + +
82F ASN 3.1 24.4 + - - -
129F SER* 5.3 5.2 - - - +
130F ILE* 1.3 80.0 - - - +
132F ASN* 1.3 73.3 + - - +
133F VAL* 3.9 9.8 + - + +
174F ASN* 3.4 17.0 - - + +
175F VAL 5.0 4.9 - - - -
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Residues in contact with ASN 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ASN* 2.9 35.3 + - + +
111F SER* 3.9 7.3 - - - -
115F CYS* 3.6 18.9 - - - -
130F ILE* 4.2 1.8 - - - +
131F VAL* 1.3 75.5 - - - +
133F VAL* 1.3 62.5 + - - +
134F GLY 3.5 3.3 + - - -
155F LEU* 4.6 19.0 + - + -
158F PHE* 4.3 8.1 - - - -
159F SER* 2.7 30.2 + - - +
173F VAL* 4.0 9.9 - - - +
174F ASN 2.9 9.1 + - - +
175F VAL* 3.2 25.8 - - - -
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Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 4.2 32.8 - - + -
18F VAL* 6.1 0.7 - - + -
81F VAL* 4.6 7.9 - - + -
82F ASN 3.1 29.9 + - - +
83F ALA* 3.9 18.3 - - + -
131F VAL* 4.5 12.1 - - + +
132F ASN* 1.3 71.9 - - - +
134F GLY* 1.3 66.8 + - - +
152F LYS* 3.7 18.2 + - - -
155F LEU* 3.8 6.7 - - - +
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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