Contacts of the strand formed by residues 417 - 426 (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 THR 417 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.5 13.5 - - + +
124B ARG* 4.6 7.0 - - + -
125B PHE 3.2 12.1 - - - +
126B LEU* 3.8 14.6 - - - +
393B CYS 3.4 12.3 - - - +
394B GLU* 5.0 3.1 - - - -
415B ASN 4.5 1.9 + - - -
416B GLN* 1.3 82.3 - - - +
418B VAL* 1.3 72.4 + - - +
419B THR* 4.8 4.7 + - - +
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Residues in contact with VAL 418 (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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123B VAL 3.9 0.3 - - - +
124B ARG* 3.3 5.2 - - - +
125B PHE* 2.9 63.1 + - + +
374B VAL* 4.3 5.8 - - + -
392B GLN 4.2 1.6 - - - +
393B CYS* 3.4 25.1 - - - +
409B CYS* 4.4 4.5 - - + -
412B VAL* 3.7 36.3 - - + -
416B GLN* 4.5 2.5 - - - +
417B THR* 1.3 76.4 - - - +
419B THR* 1.3 65.6 + - - +
420B PHE* 3.9 21.7 - - + -
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Residues in contact with THR 419 (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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122B GLN* 3.3 39.0 + - + +
123B VAL 3.5 3.4 - - - +
124B ARG* 4.5 5.2 - - - +
392B GLN* 3.0 53.2 + - - +
417B THR* 4.8 5.0 - - - +
418B VAL* 1.3 80.0 + - - +
420B PHE* 1.3 64.6 + - - +
421B TRP* 3.3 25.7 - - + +
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Residues in contact with PHE 420 (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* 6.5 0.4 - - + -
122B GLN* 3.6 2.8 - - - -
123B VAL* 2.9 42.3 + - + +
125B PHE* 4.8 5.6 - - + -
374B VAL* 3.7 34.1 - - + -
376B LEU* 4.1 35.2 - - + -
389B TYR* 5.1 5.6 - - + -
390B GLU 3.4 4.3 - - - +
391B SER* 3.4 21.1 - - - -
407B GLY* 3.4 16.8 - - - -
408B GLN* 3.2 27.4 - - - -
409B CYS* 4.3 7.9 - - - -
418B VAL* 3.9 25.1 - - + -
419B THR* 1.3 76.8 - - - +
421B TRP* 1.3 64.1 + - - +
422B VAL* 3.9 2.1 + - + -
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Residues in contact with TRP 421 (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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120B GLN* 3.6 36.2 - - + +
121B LEU 3.4 11.2 - - - +
122B GLN* 3.7 46.2 - - + -
388B SER 3.9 1.6 - - - +
389B TYR* 4.1 0.9 - - - -
390B GLU* 3.1 46.2 + - + +
392B GLN* 3.1 29.1 + - + -
399B ARG* 5.5 6.1 - - - -
419B THR* 3.3 18.0 - - + +
420B PHE* 1.3 78.0 - - - +
422B VAL* 1.3 64.9 + - - +
423B SER* 3.5 3.6 + - - -
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Residues in contact with VAL 422 (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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119B GLN 3.7 1.7 - - - +
120B GLN* 3.3 3.1 - - - -
121B LEU* 2.9 57.1 + - + +
123B VAL* 4.3 13.7 - - + -
376B LEU* 4.3 6.3 - - + -
387B ILE* 3.8 31.0 - - + -
388B SER 3.6 3.8 - - - +
389B TYR* 3.7 28.7 - - + +
420B PHE* 3.9 1.0 - - + -
421B TRP* 1.3 71.5 - - - +
423B SER* 1.3 61.2 + - - +
424B LEU* 3.9 15.4 + - + -
438B LEU* 4.4 11.4 - - + -
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Residues in contact with SER 423 (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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118B PRO* 3.9 20.1 + - - +
119B GLN 3.7 4.1 + - - -
120B GLN* 4.3 15.6 + - - +
386B HIS 3.9 0.5 - - - +
387B ILE* 3.3 6.2 - - - +
388B SER* 2.9 55.4 + - - -
421B TRP 3.5 2.4 + - - -
422B VAL* 1.3 71.4 - - - +
424B LEU* 1.3 62.9 + - - +
425B GLN* 4.0 7.3 + - - +
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Residues in contact with LEU 424 (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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111B VAL* 4.7 11.2 - - + -
113B LEU* 3.6 18.7 - - + +
118B PRO* 3.1 2.4 - - - +
119B GLN* 2.9 42.5 + - + +
121B LEU* 4.8 9.0 - - + -
385B VAL* 5.1 7.2 - - + -
386B HIS 3.8 2.9 - - - +
387B ILE* 3.6 37.7 - - + -
422B VAL* 4.1 10.1 - - + +
423B SER* 1.3 71.6 + - - +
425B GLN* 1.3 60.6 + - - +
426B ALA 4.2 0.4 - - - -
436B LEU* 4.7 14.4 - - + -
438B LEU* 6.4 1.1 - - + -
449B VAL* 4.6 14.1 - - + -
451B LEU* 3.9 27.8 - - + -
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Residues in contact with GLN 425 (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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116B GLY 6.1 2.5 - - - +
117B GLU 5.1 1.6 - - - -
118B PRO* 3.6 29.2 - - + +
385B VAL* 5.0 1.5 - - - +
386B HIS* 2.9 61.4 + - + +
387B ILE 5.2 0.6 - - - +
388B SER* 4.5 17.2 + - - -
423B SER* 4.7 6.9 + - - +
424B LEU* 1.3 73.7 - - - +
426B ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 426 (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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113B LEU* 4.3 27.2 - - + +
114B ARG 5.7 1.2 + - - -
115B PRO* 3.9 8.4 - - + +
116B GLY 3.8 20.9 + - - +
117B GLU 5.5 0.6 + - - -
384B GLY 3.7 4.7 - - - -
385B VAL* 4.2 22.0 - - + +
424B LEU 4.2 0.4 - - - -
425B GLN* 1.3 76.1 - - - +
427B THR* 1.3 64.5 + - - +
428B HIS 4.9 8.5 - - - +
430B LEU* 6.2 1.1 - - + -
451B LEU* 6.0 0.2 - - + -
453B THR* 5.3 6.7 - - - +
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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