Contacts of the strand formed by residues 141 - 145 (chain C) in PDB entry 7C17
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 THR 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C VAL* 4.4 0.7 - - - -
138C ILE 2.9 42.8 + - - +
139C ASN* 3.2 6.9 + - - +
140C GLY* 1.3 74.6 - - - +
142C GLU* 1.3 60.1 + - - +
143C ARG* 3.2 22.2 + - - +
514C PHE* 3.7 31.1 - - + -
758C ARG* 4.9 11.4 - - - +
760C ASN* 3.8 15.5 - - - +
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Residues in contact with GLU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLN* 4.5 17.9 + - + +
133C ASN* 5.5 0.9 - - - +
135C THR* 3.7 17.2 + - + +
136C PHE 3.7 4.7 - - - -
137C VAL* 4.3 11.9 - - + +
140C GLY 3.6 3.3 + - - +
141C THR* 1.3 68.6 - - - +
143C ARG* 1.3 59.3 + - - +
515C MET* 3.5 29.5 + - + +
517C GLN* 3.5 24.6 - - + +
523C GLU* 4.8 2.3 - - - +
758C ARG 3.9 5.4 - - - +
759C SER* 3.6 17.2 - - - -
760C ASN* 2.7 37.2 + - - +
765C ILE* 3.7 9.8 - - - +
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Residues in contact with ARG 143 (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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135C THR* 3.5 0.3 - - - +
136C PHE* 2.7 51.2 + - + +
138C ILE* 3.6 25.3 + - + +
139C ASN* 5.4 6.1 + - - +
141C THR* 3.3 22.4 + - - +
142C GLU* 1.3 75.2 - - - +
144C VAL* 1.3 63.4 + - - +
145C ILE* 5.7 1.6 - - + -
506C PHE* 6.4 0.2 - - + -
507C GLY* 3.0 46.9 + - - -
512C SER* 3.7 14.8 + - - +
513C GLN* 3.6 22.1 - - - +
514C PHE* 3.4 36.5 - - + -
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLN* 3.7 13.5 - - - +
134C GLY 3.6 14.6 - - - +
135C THR* 3.8 4.0 - - + -
136C PHE* 5.0 3.6 - - - -
143C ARG* 1.3 79.8 - - - +
145C ILE* 1.3 67.5 + - - +
146C VAL 3.7 0.9 + - - -
511C LEU 4.2 0.2 - - - +
513C GLN 3.6 15.4 + - - +
515C MET* 3.6 15.8 - - + +
526C HIS* 3.3 46.3 - - - +
527C LYS* 3.5 46.4 - - + +
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Residues in contact with ILE 145 (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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31C GLN* 3.0 23.0 + - - -
136C PHE* 4.8 6.3 - - + -
143C ARG* 5.7 1.6 - - + -
144C VAL* 1.3 74.0 - - - +
146C VAL* 1.3 71.7 + - - +
455C SER 6.0 0.4 - - - +
456C VAL* 3.3 23.0 - - + +
505C PHE* 3.6 48.7 - - + +
506C PHE* 3.6 35.0 - - + -
511C LEU* 3.7 24.9 - - + -
512C SER* 3.7 18.8 - - - +
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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