Contacts of the strand formed by residues 397 - 403 (chain D) in PDB entry 3RL8
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 PHE 397 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322D LEU 3.6 2.9 - - - +
323D ILE* 4.1 30.3 - - + -
375D ASN* 3.2 18.5 + - - +
395D SER* 3.3 11.2 + - - +
396D ASP* 1.3 91.5 - - + +
398D VAL* 1.3 61.4 + - - +
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Residues in contact with VAL 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D ILE 3.5 1.7 - - - +
321D LYS* 3.3 5.7 - - - +
322D LEU* 2.7 45.8 + - + +
324D LYS* 4.6 0.7 - - - -
329D LEU* 3.9 33.4 - - + -
374D VAL* 3.6 26.7 - - + -
375D ASN* 3.6 2.0 - - - +
394D THR* 3.7 19.1 - - - +
395D SER 3.6 17.9 - - - +
396D ASP 4.5 2.7 - - - +
397D PHE* 1.3 78.8 - - - +
399D TYR* 1.3 65.8 + - - +
400D LEU* 4.2 9.9 - - + -
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Residues in contact with TYR 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D GLU* 2.6 55.0 + - + +
320D ILE 3.6 6.7 - - - -
321D LYS* 4.7 20.0 - - + +
373D ALA* 3.9 2.5 - - + +
374D VAL* 3.4 5.7 - - - +
375D ASN* 2.6 46.4 + - - +
376D ASN* 4.7 19.5 - - - -
397D PHE 4.2 0.4 + - - -
398D VAL* 1.3 74.3 - - - +
400D LEU* 1.3 67.5 + - - +
401D LYS* 4.0 22.4 + - + +
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Residues in contact with LEU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D MET 3.8 0.2 - - - +
319D GLU* 3.5 1.6 - - - -
320D ILE* 2.7 48.8 + - + +
322D LEU* 3.9 19.1 - - + -
331D PHE* 3.9 28.7 - - + -
365D LEU* 4.1 19.3 - - + -
371D LEU* 4.4 13.5 - - + -
373D ALA 3.7 11.4 - - - +
374D VAL* 4.1 18.6 - - + -
391D LEU* 4.1 17.0 - - + -
398D VAL* 4.2 9.9 - - + -
399D TYR* 1.3 75.8 - - - +
401D LYS* 1.3 60.7 + - - +
402D VAL* 3.7 8.9 + - + +
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Residues in contact with LYS 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ILE* 4.2 30.4 - - + +
318D MET 3.7 3.8 - - - +
319D GLU* 5.0 2.0 - - + -
371D LEU* 3.8 1.0 - - - +
372D LEU* 2.9 49.8 + - + -
373D ALA* 3.1 31.7 + - + +
399D TYR* 4.0 29.0 + - + +
400D LEU* 1.3 71.2 - - - +
402D VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ILE* 3.4 4.9 - - - +
318D MET* 2.8 69.5 + - + +
320D ILE* 4.0 10.1 - - + -
365D LEU* 3.9 12.8 - - + -
369D ASP* 4.4 16.8 - - + +
370D LYS 3.2 11.0 - - - +
371D LEU* 3.7 23.6 - - + -
372D LEU* 4.3 5.4 - - - +
400D LEU* 4.0 16.4 - - + +
401D LYS* 1.3 81.6 - - - +
403D ALA* 1.3 60.7 + - - +
404D LYS* 4.7 0.7 - - + -
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Residues in contact with ALA 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D LYS* 3.2 24.7 - - + +
317D ILE* 4.7 1.3 - - + -
369D ASP* 3.9 2.1 - - - +
370D LYS* 2.9 46.0 + - + +
372D LEU* 4.1 25.6 - - + +
402D VAL* 1.3 72.9 - - - +
404D LYS* 1.3 62.9 + - - +
405D PRO* 3.9 2.9 - - - +
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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