Contacts of the strand formed by residues 396 - 401 (chain B) in PDB entry 1G88
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 ASP 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B CYS* 3.1 7.6 - - - -
392B LYS* 2.7 49.4 + - + +
393B GLY* 5.3 2.7 - - - -
394B GLU 5.0 1.6 + - - -
395B GLY* 1.3 78.5 + - - +
397B VAL* 1.3 60.4 + - - +
398B TRP* 4.6 8.6 + - - +
436B LYS* 3.6 15.7 + - - -
438B PHE* 3.4 11.4 - - - +
439B ASP* 3.2 20.9 - - - +
440B LEU* 3.4 21.3 + - - +
441B ARG* 6.0 0.2 - - - +
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Residues in contact with VAL 397 (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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323B TRP* 3.8 30.1 - - + -
389B LEU* 4.9 8.7 - - + -
390B GLU 3.3 6.3 - - - +
395B GLY 3.8 9.6 + - - +
396B ASP* 1.3 80.3 - - - +
398B TRP* 1.3 73.8 + - - +
436B LYS* 3.7 2.9 - - - -
437B VAL* 2.9 38.5 + - + +
438B PHE* 3.1 24.7 + - + +
501B LEU* 3.9 10.8 - - + -
527B ILE* 6.1 1.3 - - + -
529B LEU* 4.1 21.1 - - + -
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Residues in contact with TRP 398 (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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388B GLN 3.4 0.4 - - - +
389B LEU* 3.3 6.4 - - - -
390B GLU* 2.7 39.1 + - + +
392B LYS* 3.2 48.5 - - + +
396B ASP* 4.6 4.8 + - - +
397B VAL* 1.3 85.2 - - - +
399B VAL* 1.3 63.4 + - - +
434B TYR* 3.7 51.4 - + + +
435B ILE* 3.4 10.8 - - - -
436B LYS* 3.0 53.9 - - + +
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Residues in contact with VAL 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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387B VAL* 4.7 7.4 - - + -
388B GLN 3.2 3.4 - - - +
389B LEU* 3.4 26.2 - - + -
397B VAL* 5.3 0.2 - - + -
398B TRP* 1.3 74.8 - - - +
400B ARG* 1.3 71.8 + - - +
401B CYS 4.1 3.1 - - - +
407B VAL* 5.7 1.1 - - + -
409B VAL* 5.0 0.4 - - + -
429B ILE* 3.7 27.4 - - + -
433B ALA 3.7 0.7 - - - +
434B TYR* 3.4 7.4 - - - -
435B ILE* 3.2 35.1 + - - +
437B VAL* 4.0 20.9 - - + -
501B LEU* 6.1 0.4 - - + -
503B MET* 3.5 22.9 - - + -
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Residues in contact with ARG 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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387B VAL* 3.3 1.7 - - - -
388B GLN* 2.9 60.9 + - + +
390B GLU* 3.8 8.7 + - - -
399B VAL* 1.3 77.6 - - - +
401B CYS* 1.3 60.1 + - - +
402B LEU* 3.1 33.1 + - + +
432B SER* 5.1 5.2 + - - +
433B ALA 3.6 8.1 - - - +
434B TYR* 3.1 59.7 - - + +
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Residues in contact with CYS 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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386B GLY 4.2 2.5 - - - -
387B VAL* 4.2 4.5 - - + -
399B VAL* 4.0 3.6 - - + +
400B ARG* 1.3 70.0 - - - +
402B LEU* 1.3 60.3 + - - +
403B SER 4.0 6.1 - - - -
405B HIS 3.4 26.2 - - - -
407B VAL* 3.7 21.8 - - + -
429B ILE* 3.6 30.3 - - + -
430B TYR 3.7 7.6 - - - +
431B PRO* 3.8 13.7 - - - -
432B SER* 2.7 32.8 + - - +
433B ALA 3.2 9.6 + - - +
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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