Contacts of the strand formed by residues 318 - 322 (chain C) in PDB entry 1EQB
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 LEU 318 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ALA* 3.8 16.8 - - + -
174C PHE* 5.5 0.9 - - + -
175C SER 3.6 24.7 - - - +
176C ALA* 4.3 6.5 - - - +
177C TYR 3.5 34.1 - - - +
178C SER* 3.3 4.0 - - - +
203C HIS* 3.6 24.2 - - + -
295C ALA* 5.4 0.2 - - - -
314C THR* 2.7 25.9 + - - -
316C ASN* 2.9 14.6 + - - +
317C HIS* 1.3 88.2 - - + +
319C PHE* 1.3 75.0 + - - +
320C LEU* 5.8 0.2 - - + -
363C ARG* 4.2 8.5 - - + -
364C VAL 3.1 13.7 - - - +
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Residues in contact with PHE 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C SER* 4.2 7.0 - - - -
295C ALA* 3.9 11.4 - - + -
298C MET* 3.8 30.7 - - + -
299C VAL* 3.4 31.9 - - + -
302C PHE* 4.2 17.9 - + - -
309C VAL* 4.3 13.7 - - + -
310C VAL 5.6 0.2 - - - +
313C GLY 4.7 0.4 - - - +
314C THR* 4.3 5.2 - - + -
317C HIS 5.5 0.2 - - - -
318C LEU* 1.3 88.4 - - - +
320C LEU* 1.3 65.8 + - - +
321C VAL* 3.6 27.6 - - + -
363C ARG* 3.7 2.8 - - - +
364C VAL* 2.9 66.0 + - + -
366C THR* 5.4 1.6 - - + -
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ALA 5.2 2.2 - - - +
123C HIS 6.1 0.9 - - - -
124C GLY* 5.9 1.1 - - - +
176C ALA* 3.7 28.7 - - + +
178C SER* 5.5 0.6 - - - -
309C VAL* 3.3 10.8 - - - +
310C VAL* 3.1 55.2 + - + +
318C LEU* 5.8 0.4 - - + -
319C PHE* 1.3 74.5 - - - +
321C VAL* 1.3 62.7 + - - +
322C ASP 4.0 0.7 - - - -
347C ASN* 3.9 20.2 - - + +
348C SER 4.0 15.9 - - - +
349C VAL* 4.3 13.0 - - + -
350C PRO* 4.5 5.8 - - + -
362C ILE 3.6 2.2 - - - +
363C ARG* 3.7 35.7 - - + -
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Residues in contact with VAL 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C PHE* 3.7 25.8 - - + -
307C TYR* 4.3 17.0 - - + -
308C LYS 3.5 7.6 - - - +
309C VAL* 4.6 5.4 - - + -
319C PHE* 3.6 29.8 - - + -
320C LEU* 1.3 72.5 - - - +
322C ASP* 1.3 61.1 + - - +
323C LEU* 3.4 25.3 + - + +
349C VAL* 4.8 2.0 - - - -
361C GLY* 3.1 24.8 - - - -
362C ILE* 2.9 31.3 + - + +
364C VAL* 4.8 0.4 - - + -
390C LEU* 5.1 0.2 - - + -
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Residues in contact with ASP 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR* 5.5 0.5 - - - -
308C LYS* 2.8 58.4 + - + +
310C VAL* 4.4 13.4 - - + +
320C LEU 4.0 1.8 + - - -
321C VAL* 1.3 70.8 - - - +
323C LEU* 1.3 62.2 + - - +
324C VAL* 3.0 32.3 + - - +
325C ASP* 3.5 14.7 + - - +
326C LYS* 5.2 0.9 - - - +
349C VAL* 3.6 28.0 - - - +
350C PRO* 4.6 5.7 - - - +
360C SER 3.9 3.3 - - - +
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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
------------------------------------------------------------
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