Contacts of the strand formed by residues 321 - 325 (chain A) in PDB entry 1H41
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 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A HIS* 4.4 8.3 - - + -
240A TYR* 4.0 9.2 - - + +
283A GLY 3.0 16.2 + - - +
284A GLY* 3.2 4.5 - - - -
285A PHE 3.0 24.1 + - - +
315A LEU* 3.3 2.6 - - - +
319A GLY 4.5 6.1 - - - +
320A GLY* 1.3 78.2 - - - +
322A VAL* 1.3 62.8 + - - +
323A PHE* 3.7 30.3 - - + -
354A ASN* 3.3 16.6 - - + +
356A ILE* 4.1 7.6 - - + -
438A HIS* 3.7 33.7 - - + +
1732A CO 4.5 2.2 - - - +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PHE* 3.5 5.2 - - + +
287A VAL* 3.9 25.4 - - + -
308A ALA* 4.2 6.7 - - + +
311A LEU* 3.9 9.6 - - + -
312A ALA* 3.6 37.2 - - + +
315A LEU* 3.9 12.1 - - + -
321A VAL* 1.3 74.1 - - - +
323A PHE* 1.3 64.3 + - - +
324A TRP* 3.6 18.1 + - + +
354A ASN 2.9 9.4 + - - +
355A VAL* 4.0 7.4 - - + +
356A ILE* 2.8 33.3 + - - +
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Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A HIS* 4.2 9.6 - + + -
156A VAL* 4.2 22.7 - - + -
158A ASN* 5.9 0.2 - - - -
206A VAL* 4.6 8.1 - - + -
240A TYR* 3.4 47.3 - + - -
285A PHE 2.8 19.1 + - - +
286A LEU* 3.3 23.7 - - + +
287A VAL* 2.9 25.6 + - - +
321A VAL* 3.7 14.6 - - + -
322A VAL* 1.3 71.0 - - - +
324A TRP* 1.3 59.6 + - - +
325A ARG 3.9 0.4 - - - -
356A ILE* 3.4 20.9 - - + +
358A GLN* 3.7 14.1 - - + +
385A MET* 3.2 33.9 - - + -
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Residues in contact with TRP 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PHE* 4.3 3.4 - + - -
287A VAL* 3.6 30.7 - - + -
289A ALA* 3.7 22.1 - - + +
297A PRO* 3.8 24.9 - - + -
304A HIS* 2.8 49.9 - + + +
307A GLY 3.8 4.0 - - - -
308A ALA* 3.5 37.2 - - + -
311A LEU* 4.0 9.9 - - + -
322A VAL* 3.6 5.3 + - + -
323A PHE* 1.3 71.6 - - - +
325A ARG* 1.3 72.9 + - - +
326A ALA 3.5 0.3 + - - -
344A PHE* 4.1 4.7 - + - -
351A PHE* 5.0 0.7 - + - -
355A VAL* 4.3 12.3 - - + -
356A ILE 2.9 10.7 + - - +
357A LEU* 3.4 28.4 - - + +
358A GLN 2.9 22.3 + - - -
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Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN* 5.5 0.4 + - - -
160A TRP* 3.9 5.2 - - - -
210A VAL* 3.9 22.1 - - - +
286A LEU* 3.7 28.5 - - + -
287A VAL 2.9 23.8 + - - +
288A LYS* 3.5 27.5 - - + +
289A ALA 5.4 3.5 + - - +
304A HIS* 5.0 1.6 + - - -
324A TRP* 1.3 87.1 + - - +
326A ALA* 1.3 64.2 + - - +
344A PHE* 4.3 1.7 - - - -
358A GLN* 3.4 9.9 - - + +
360A LYS* 3.5 10.5 - - - +
387A GLU* 2.9 41.4 + - - +
1713A GCV 2.8 43.4 + - - -
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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