Contacts of the strand formed by residues 398 - 407 (chain B) in PDB entry 4EGA
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 398 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B TRP* 3.5 7.3 - - - -
363B TYR 2.9 35.3 + - - +
365B ILE* 3.4 29.2 - - + +
396B VAL* 6.0 1.6 - - - +
397B VAL* 1.3 74.2 - - - +
399B TRP* 1.3 76.1 + - - +
400B VAL* 3.8 10.2 + - + +
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Residues in contact with TRP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B GLU* 3.6 41.3 + - + +
361B GLY* 3.6 32.5 - - - -
362B TRP* 3.6 53.5 - + + -
373B PRO* 5.9 3.8 - - + -
398B THR* 1.3 86.8 - - - +
400B VAL* 1.3 69.9 + - - +
401B SER* 5.2 3.4 - - - -
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B TYR* 3.7 24.7 - - + -
360B GLU* 3.7 2.9 - - - -
361B GLY 3.0 32.4 + - - +
363B TYR* 3.4 35.7 - - + -
365B ILE* 6.1 0.2 - - + -
398B THR* 3.8 13.5 - - + +
399B TRP* 1.3 87.4 + - - +
401B SER* 1.3 64.6 - - - +
402B GLU* 4.3 22.0 - - + +
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Residues in contact with SER 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ARG* 2.8 41.3 + - - +
359B TYR 3.4 6.3 - - - -
360B GLU* 4.0 15.4 - - - +
399B TRP* 5.2 3.8 - - - -
400B VAL* 1.3 79.0 - - - +
402B GLU* 1.3 56.7 + - - +
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Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ARG* 3.9 6.3 - - - +
359B TYR* 3.0 33.0 + - + +
363B TYR* 4.5 22.0 - - - -
370B PHE* 4.8 7.3 - - + -
400B VAL* 4.3 23.8 - - + +
401B SER* 1.3 75.6 - - - +
403B GLU* 1.3 69.1 + - - +
404B ASN* 4.3 4.6 - - + +
452B ALA* 3.4 30.0 - - - +
455B THR* 4.9 2.8 + - - -
469B HIS* 5.9 1.1 + - - +
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B LEU* 3.9 30.7 - - + +
357B GLY 3.3 9.6 - - - +
358B ARG* 4.0 28.9 + - + +
402B GLU* 1.3 80.9 - - - +
404B ASN* 1.3 63.7 + - - +
466B ASN* 4.7 3.6 + - - -
469B HIS* 3.1 40.3 + - - +
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Residues in contact with ASN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B LEU* 3.9 6.5 - - - +
357B GLY* 2.8 31.9 + - - +
359B TYR* 4.7 10.7 - - + +
370B PHE* 3.8 19.8 - - + -
402B GLU* 4.3 10.3 + - + +
403B GLU* 1.3 77.7 + - - +
405B TYR* 1.3 68.2 + - - +
406B MET* 3.6 15.2 + - + +
448B SER* 2.8 25.4 + - - -
450B SER* 2.9 37.7 + - - -
451B ARG* 4.3 4.6 - - - +
469B HIS* 4.9 0.6 - - - -
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Residues in contact with TYR 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B TRP* 3.5 37.2 - + + -
349B GLU* 5.4 9.9 - - + -
354B ILE* 4.0 13.7 - - + -
355B TYR 3.5 8.7 - - - -
356B LEU* 3.8 33.5 - - + +
404B ASN* 1.3 77.5 - - - +
406B MET* 1.3 60.4 + - - +
449B VAL* 2.9 25.9 + - + -
450B SER* 3.0 29.3 + - - -
463B VAL* 3.6 23.2 - - + +
464B PRO 5.2 1.0 + - - -
466B ASN* 2.9 36.4 + - - +
469B HIS* 4.3 9.6 - + + -
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Residues in contact with MET 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ASP 3.8 0.3 - - - +
354B ILE* 3.2 7.1 - - - +
355B TYR* 3.0 67.2 + - + +
357B GLY* 5.8 0.7 - - - +
359B TYR* 6.5 0.4 - - - -
404B ASN* 3.8 14.8 - - + +
405B TYR* 1.3 75.5 - - - +
407B PHE* 1.3 61.3 + - - +
446B ASP* 3.9 37.2 - - + +
447B LEU 3.5 3.6 - - - -
448B SER* 3.6 28.3 - - - +
449B VAL* 4.2 3.6 - - - -
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Residues in contact with PHE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B LEU* 4.2 5.8 - - + -
353B ASP* 3.4 30.5 - - + -
354B ILE* 4.0 14.6 - - + -
406B MET* 1.3 74.3 - - - +
408B ARG* 1.3 52.2 + - - +
409B LEU* 2.7 44.1 + - + -
412B PHE* 3.7 18.6 - + - -
446B ASP* 3.3 4.0 - - - +
447B LEU* 2.7 45.0 + - + +
449B VAL* 3.7 17.9 - - + +
529B ALA* 3.8 26.7 - - + -
530B PHE* 3.5 37.5 - + - -
533B SER* 4.1 9.2 - - - -
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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