Contacts of the strand formed by residues 487 - 495 (chain A) in PDB entry 4QYJ
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 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LEU* 4.4 4.2 - - + +
156A ARG* 2.5 48.9 + - + +
157A VAL 2.8 20.0 + - - +
159A VAL* 3.7 9.0 - - - +
185A CYS* 3.4 15.4 + - - +
483A ILE* 3.1 20.0 + - - +
484A GLU 3.2 17.5 - - - +
485A HIS 4.4 0.7 - - - -
486A TYR* 1.3 79.9 + - - +
488A THR* 1.3 79.3 + - - +
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Residues in contact with THR 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.4 5.2 - - - +
157A VAL* 3.1 24.9 + - + +
158A PRO 4.6 6.1 - - - +
159A VAL* 4.7 11.4 - - + -
487A THR* 1.3 91.7 - - - +
489A THR* 1.3 67.0 + - - +
469B PHE* 3.7 29.4 - - + -
476B ARG* 3.7 19.8 + - - +
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Residues in contact with THR 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLY* 5.4 0.4 - - - -
154A THR* 4.0 31.2 - - + +
155A GLN 3.3 9.9 - - - +
156A ARG* 3.6 33.7 - - - +
157A VAL* 4.6 0.9 - - - -
488A THR* 1.3 83.8 + - - +
490A ARG* 1.3 64.2 + - - +
491A SER* 5.5 0.2 + - - -
465B PRO* 4.7 6.1 - - - +
469B PHE* 4.1 0.3 - - - -
476B ARG* 2.9 44.6 + - - +
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A THR* 3.3 2.7 - - - -
155A GLN* 2.9 44.2 + - + +
157A VAL* 3.8 27.1 - - + -
489A THR* 1.3 76.9 - - - +
491A SER* 1.3 64.5 + - - +
492A LEU* 4.1 0.9 + - - +
444B ASN* 2.4 40.4 + - - +
445B ASP* 4.3 6.1 + - - +
447B LEU* 3.0 27.1 + - - +
448B GLU* 5.4 0.4 - - - +
449B ALA 2.8 27.9 + - - +
450B GLY 3.6 10.1 - - - +
452B VAL* 3.6 17.5 - - - +
469B PHE* 3.7 21.5 - - + -
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER 3.5 3.8 - - - -
154A THR* 3.6 15.8 - - - +
489A THR* 5.5 0.5 + - - -
490A ARG* 1.3 78.1 - - - +
492A LEU* 1.3 61.2 + - - +
493A VAL* 5.6 0.9 - - - -
444B ASN* 4.8 1.7 + - - -
450B GLY 3.0 7.9 + - - +
451B THR* 3.9 16.8 - - - -
452B VAL* 3.1 27.0 + - - +
464B LEU* 3.4 24.6 - - - +
465B PRO* 3.0 24.4 + - - +
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG 3.8 1.2 - - - +
152A ALA* 3.2 3.1 - - - -
153A SER* 2.8 53.4 + - - +
155A GLN* 6.5 0.9 - - + -
490A ARG 5.3 0.4 - - - +
491A SER* 1.3 76.0 - - - +
493A VAL* 1.3 64.1 + - - +
494A ILE* 4.1 23.1 - - + -
441B LEU* 4.8 12.1 - - + -
444B ASN* 3.6 38.1 - - + +
452B VAL* 3.5 11.4 - - + +
454B VAL* 4.1 23.3 - - + -
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Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 4.2 9.6 - - + -
142A LEU* 5.1 4.7 - - + -
144A LEU* 6.1 0.7 - - + -
150A SER* 4.9 11.4 - - - -
151A ARG 3.7 3.4 - - - +
152A ALA* 3.7 22.4 - - + -
491A SER* 5.6 0.9 - - - -
492A LEU* 1.3 77.2 - - - +
494A ILE* 1.3 65.9 + - - +
495A ALA* 3.9 0.4 + - + -
452B VAL 3.2 7.4 + - - +
453B TRP* 3.3 26.5 - - + +
454B VAL 2.8 24.1 + - - +
456B THR* 4.4 9.7 - - + +
459B MET* 4.9 6.7 - - + +
464B LEU* 4.0 30.1 - - + -
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Residues in contact with ILE 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER* 3.2 25.7 - - - -
151A ARG* 3.0 22.2 + - + +
492A LEU* 4.1 28.0 - - + -
493A VAL* 1.3 74.4 - - - +
495A ALA* 1.3 65.3 + - - +
496A TYR* 3.5 6.0 - - + -
441B LEU* 4.8 12.6 - - + -
454B VAL* 3.7 20.9 - - + -
437C LEU* 3.5 44.9 - - + -
441C LEU* 4.4 14.6 - - + -
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Residues in contact with ALA 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 4.0 23.1 - - + -
148A VAL* 4.6 5.4 - - + -
149A ARG 3.7 5.4 - - - +
150A SER* 4.6 1.1 - - - +
493A VAL* 3.9 1.4 + - + -
494A ILE* 1.3 71.7 - - - +
496A TYR* 1.3 60.6 + - - +
454B VAL 2.7 12.4 + - - +
455B ASN* 3.2 53.2 + - + +
456B THR* 4.1 8.6 - - + +
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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