Contacts of the strand formed by residues 321 - 325 (chain A) in PDB entry 2E4Y
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 ILE 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ILE* 4.4 15.9 - - + -
208A PHE* 5.4 1.1 - - + -
210A TRP* 4.6 9.4 - - + -
296A THR* 5.5 2.6 - - + +
297A TRP 2.5 18.5 + - - +
298A VAL* 2.8 21.1 - - + +
299A ALA 2.8 21.8 + - - -
319A GLY 5.1 0.4 - - - +
320A ALA* 1.3 79.2 - - - +
322A THR* 1.3 65.5 + - - +
323A LEU* 6.0 1.3 - - + -
468A VAL* 4.1 20.9 - - + -
469A PHE 3.1 13.7 - - - +
470A ASN* 4.5 8.3 - - + +
483A VAL* 5.9 1.3 - - + -
492A LEU* 6.1 1.3 - - + -
497A ILE* 4.3 12.8 - - + -
499A TRP* 3.5 39.7 - - + -
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Residues in contact with THR 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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297A TRP 4.8 1.3 - - - +
299A ALA* 3.2 29.2 - - + +
303A TRP* 3.6 31.0 - - + +
304A GLY* 2.6 26.2 + - - -
320A ALA* 4.3 1.3 - - + -
321A ILE* 1.3 83.6 - - - +
323A LEU* 1.3 62.4 + - - +
469A PHE* 2.8 40.2 + - - +
471A LEU* 5.8 1.2 + - + +
480A TYR* 3.6 12.2 - - + -
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLN* 3.8 27.1 - - + +
200A ALA* 3.9 20.4 - - + +
201A MET* 3.5 34.5 - - + +
204A ILE* 4.4 7.2 - - + -
299A ALA 2.9 11.1 + - - +
300A SER* 4.8 0.2 - - - -
301A ASP* 3.0 24.4 - - - -
304A GLY* 3.5 8.3 - - - -
321A ILE* 6.0 0.9 - - + -
322A THR* 1.3 73.5 - - - +
324A GLU* 1.3 62.9 + - - +
466A TYR* 4.5 9.9 - - + -
467A ASN 3.2 17.7 - - - +
468A VAL* 3.5 32.8 - - + -
486A TRP* 5.7 0.2 - - + -
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Residues in contact with GLU 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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64A ARG* 4.0 8.0 + - - -
301A ASP* 3.6 10.4 - - - +
304A GLY* 3.7 19.7 - - - -
305A ALA* 3.8 12.2 + - + +
306A GLN* 5.6 0.3 - - - +
323A LEU* 1.3 74.8 - - - +
325A LEU* 1.3 86.0 + - - +
387A GLU* 4.9 1.0 - - - +
388A SER* 3.0 35.6 + - - +
389A LYS* 2.7 32.4 + - - +
466A TYR* 3.2 8.5 - - - +
467A ASN* 2.7 31.9 + - + +
469A PHE* 4.7 17.0 - - + -
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Residues in contact with LEU 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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174A THR* 4.4 9.9 - - + -
191A VAL* 3.3 42.2 - - + -
192A PRO* 3.8 11.7 - - + -
197A GLN* 5.3 0.2 - - - +
301A ASP* 4.9 9.2 - - + +
324A GLU* 1.3 99.2 + - + +
326A ALA* 1.3 65.1 + - - +
327A SER* 3.2 8.5 + - - -
388A SER* 4.0 0.8 + - - +
389A LYS* 4.1 15.5 - - + +
392A PHE* 3.6 21.8 - - + -
465A ARG 3.7 3.8 - - - +
466A TYR* 3.2 36.3 - - + -
467A ASN* 3.7 6.3 + - - -
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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
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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