Contacts of the strand formed by residues 435 - 441 (chain B) in PDB entry 3V4P
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 435 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG* 5.4 4.0 - - - +
379B SER* 4.7 2.3 + - - -
380B SER 5.2 0.3 - - - +
382B PRO* 5.6 0.3 - - - +
433B PRO* 4.3 22.0 - - + -
434B HIS* 1.3 77.9 - - - +
436B LEU* 1.3 68.7 + - - +
437B ARG* 5.6 3.4 - - + +
448B ILE* 4.4 19.1 - - + -
449B VAL 3.6 10.5 - - - +
450B GLU* 4.6 19.1 - - + +
451B LEU 4.9 0.2 - - - +
452B HIS* 6.3 0.2 - - + -
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS* 5.8 2.9 - - + -
379B SER* 3.8 11.7 - - - +
380B SER 3.2 28.9 - - - +
381B LEU* 4.5 14.8 - - + -
382B PRO* 3.6 21.8 - - + -
385B VAL* 5.1 1.8 - - + -
387B ILE* 5.7 2.0 - - + -
424B LEU* 4.7 19.1 - - + -
434B HIS 4.6 3.8 - - - +
435B LEU* 1.3 80.1 - - - +
437B ARG* 1.3 65.1 + - - +
438B LEU* 4.2 6.7 - - + -
447B LEU 3.7 1.0 - - - +
448B ILE* 3.7 4.3 - - - +
449B VAL* 2.9 47.5 + - + +
451B LEU* 4.1 23.1 - - + -
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Residues in contact with ARG 437 (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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377B GLU 3.6 1.0 - - - +
378B HIS* 3.3 5.0 - - - -
379B SER* 3.2 41.5 + - - +
435B LEU* 5.6 3.1 - - + +
436B LEU* 1.3 79.0 - - - +
438B LEU* 1.3 62.6 + - - +
439B ARG* 3.7 5.3 + - + +
446B GLU* 3.2 33.5 + - - +
447B LEU 3.7 2.7 - - - -
448B ILE* 4.0 18.5 - - + +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.1 2.6 - - - +
121B LEU* 4.8 4.7 - - + -
123B VAL* 4.9 1.3 - - + -
376B LEU* 3.7 15.3 - - + +
377B GLU 3.2 3.4 - - - +
378B HIS* 3.5 17.9 - - + -
387B ILE* 4.4 7.6 - - + -
389B TYR* 3.2 30.1 - - + +
422B VAL* 4.4 22.2 - - + -
424B LEU* 6.4 1.3 - - + -
436B LEU* 5.5 4.7 - - + -
437B ARG* 1.3 71.4 - - - +
439B ARG* 1.3 62.2 + - - +
446B GLU* 3.8 1.9 - - - -
447B LEU* 2.9 65.9 + - + +
449B VAL* 4.0 16.6 - - + -
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Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B SER* 2.9 47.4 + - - -
320B ALA* 4.1 7.0 + - - +
322B ASN* 4.1 21.1 + - - +
376B LEU* 3.2 6.0 - - - +
377B GLU* 2.9 55.9 + - + +
378B HIS 4.2 19.8 + - - -
379B SER* 5.0 6.5 - - - +
437B ARG* 3.7 4.8 + - + +
438B LEU* 1.3 73.9 - - - +
440B ALA* 1.3 61.3 + - - +
441B LEU* 3.6 7.6 + - - +
443B PHE 5.8 1.6 - - - +
445B GLU 4.0 8.1 - - - +
446B GLU* 4.0 23.3 - - + +
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Residues in contact with ALA 440 (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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104B LEU* 5.1 8.4 - - + +
125B PHE* 4.3 19.1 - - + -
322B ASN* 4.0 1.5 - - - +
374B VAL* 5.3 3.6 - - + -
375B THR 3.3 10.3 - - - +
376B LEU* 4.6 4.3 - - + +
439B ARG* 1.3 71.9 - - - +
441B LEU* 1.3 56.1 + - - +
442B GLY 3.2 0.2 + - - -
443B PHE* 2.8 58.1 + - + +
445B GLU* 3.5 13.4 + - + +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B SER* 4.5 14.1 - - - +
322B ASN* 3.6 28.9 - - - +
323B ILE 5.2 5.2 - - - +
324B GLN* 5.4 2.7 - - + -
345B PRO* 3.6 36.6 - - + +
346B LYS* 3.0 37.8 + - + +
375B THR* 2.9 20.5 + - + +
377B GLU* 3.5 37.0 - - - +
439B ARG* 3.6 7.7 + - - +
440B ALA* 1.3 70.4 - - - +
442B GLY* 1.3 64.0 + - - +
443B PHE* 3.6 4.7 - - - -
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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