Contacts of the strand formed by residues 339 - 344 (chain E) in PDB entry 4IG9
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 339 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255E LYS* 5.0 0.7 - - - -
256E ILE* 3.2 21.8 - - + +
258E VAL* 4.0 19.5 - - + -
330E ILE* 3.7 25.6 - - + +
334E ASP* 3.7 46.0 - - + +
337E GLY* 3.5 6.2 - - - +
338E LYS* 1.3 79.9 - - - +
340E LEU* 1.3 58.8 + - - +
341E ARG 3.3 21.5 - - - +
342E ASN* 4.3 7.0 - - + -
356E ILE* 4.2 10.3 - - + -
358E ARG* 3.3 27.6 + - + +
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Residues in contact with LEU 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E LYS* 3.7 18.8 - - + +
256E ILE 2.6 18.7 + - - +
257E ILE* 3.7 18.4 - - + -
338E LYS 3.6 1.6 + - - -
339E LEU* 1.3 74.5 - - - +
341E ARG* 1.3 67.5 + - - +
358E ARG* 2.6 42.3 + - - +
428E TYR* 5.2 4.5 - - + -
429E ASP* 3.3 35.4 - - + +
432E GLU* 4.1 18.8 - - + +
433E VAL* 3.8 28.3 - - - +
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Residues in contact with ARG 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E ILE 3.4 0.6 + - - -
257E ILE* 3.4 6.0 - - + +
258E VAL 2.9 25.3 + - - -
339E LEU* 3.3 9.1 - - - +
340E LEU* 1.3 86.6 + - - +
342E ASN* 1.3 59.9 + - - +
343E TYR* 3.5 23.3 - - + +
358E ARG* 3.6 47.8 - - - +
359E ILE 4.8 1.0 + - - -
360E ILE* 3.4 32.5 - - - +
421E GLN* 5.2 5.5 + - - +
424E ARG* 5.0 10.5 - - - +
425E ALA* 3.6 24.6 - - - +
428E TYR* 6.1 1.4 - - - -
429E ASP* 3.1 31.5 + - - +
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Residues in contact with ASN 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E VAL 2.8 17.8 - - - +
260E THR* 3.5 18.8 + - - +
330E ILE* 4.0 25.1 - - + +
339E LEU* 4.3 5.2 - - + -
341E ARG* 1.3 74.0 - - - +
343E TYR* 1.3 62.5 + - - +
344E THR* 3.6 1.1 + - - +
351E GLU* 3.4 33.7 + - - +
356E ILE* 3.8 16.2 - - + +
358E ARG 3.0 16.2 + - - +
359E ILE* 3.6 9.0 - - + +
360E ILE 3.1 21.3 + - - +
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Residues in contact with TYR 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E ILE* 3.9 15.9 - - + -
258E VAL 3.2 5.2 + - - +
259E LEU* 3.3 30.9 - - + +
260E THR 3.0 23.7 + - - +
341E ARG* 3.5 23.3 - - + -
342E ASN* 1.3 71.7 - - - +
344E THR* 1.3 58.8 + - - +
360E ILE* 3.4 38.1 - - + +
362E CYS* 4.5 1.3 - - - -
422E PHE* 3.8 26.2 - + - -
425E ALA* 3.5 6.1 - - + +
426E MET* 3.5 33.2 + - + -
429E ASP* 2.5 26.7 + - - -
448E VAL* 4.3 7.7 - - + +
451E ILE* 3.9 11.0 - - + -
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Residues in contact with THR 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E THR* 3.1 28.5 + - - -
342E ASN* 4.4 5.4 - - - +
343E TYR* 1.3 73.9 - - - +
345E GLN* 1.3 69.2 + - - +
346E ASN* 2.9 27.1 + - - +
351E GLU* 3.8 15.9 + - - +
359E ILE* 4.7 1.6 - - + -
360E ILE 3.1 13.8 + - - +
361E GLN* 4.0 25.5 - - + +
362E CYS* 3.2 29.6 + - - +
448E VAL* 4.4 4.2 - - - +
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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