Contacts of the strand formed by residues 521 - 531 (chain D) in PDB entry 4JF7
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 ALA 521 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D LEU* 3.6 23.3 - - + -
495D ARG* 3.1 31.5 + - - +
498D PRO* 4.0 22.7 - - + -
519D GLN 3.7 0.4 + - - -
520D GLU* 1.3 79.9 - - - +
522D ALA* 1.3 62.2 + - - +
543D ILE* 4.4 3.6 - - + -
544D GLU 3.2 15.5 - - - +
545D LEU* 4.0 4.3 - - + -
546D SER 4.4 1.8 - - - +
553D PHE* 4.4 5.2 - - - -
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Residues in contact with ALA 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ARG* 3.7 13.9 - - - +
462D VAL* 3.9 10.7 - - - +
463D TYR 4.1 1.9 - - - +
489D LEU* 3.6 23.7 - - - +
495D ARG* 4.3 13.5 - - - +
521D ALA* 1.3 77.2 - - - +
523D TYR* 1.3 70.6 + - + +
524D GLY 3.9 0.3 + - - -
543D ILE* 5.5 1.1 - - - +
544D GLU* 3.0 27.9 + - + +
553D PHE* 4.2 11.2 - - + -
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Residues in contact with TYR 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ARG* 3.5 17.1 + - - -
164D ILE* 3.7 27.5 - - + +
165D PRO* 4.9 1.5 - - + +
291D THR* 4.3 10.3 - - - -
390D GLU* 2.8 41.6 + - - -
405D ARG* 3.1 16.4 + - - -
462D VAL* 3.8 15.3 - - + -
463D TYR* 3.3 30.1 - + + +
495D ARG* 4.6 7.0 - - - -
522D ALA* 1.3 82.1 - - + +
524D GLY* 1.3 58.3 + - - +
525D HIS* 4.6 11.9 - + + +
542D ILE 3.8 1.0 - - - +
543D ILE* 3.6 3.5 - - - +
544D GLU* 2.9 49.4 + - + +
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Residues in contact with GLY 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D TYR* 3.3 12.3 + - - -
464D ALA* 3.7 3.4 - - - +
465D ASP* 3.2 27.4 + - - +
487D SER* 3.6 23.1 + - - -
522D ALA 3.9 0.4 + - - -
523D TYR* 1.3 77.1 - - - +
525D HIS* 1.3 64.1 + - - -
526D THR* 4.8 0.6 + - - -
542D ILE 3.2 8.5 - - - -
543D ILE* 4.5 2.2 - - - -
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Residues in contact with HIS 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D PRO* 3.3 45.8 + - + +
166D SER* 4.4 9.2 - - - -
167D PHE* 4.5 8.7 - - + -
291D THR* 3.7 15.2 + - - -
292D GLY* 4.2 7.2 + - - -
293D SER 4.9 0.4 - - - -
392D ARG* 4.2 10.3 - - - +
463D TYR* 3.3 44.1 + + - -
465D ASP* 3.2 8.5 - - - +
523D TYR* 4.6 6.1 - + + -
524D GLY* 1.3 73.5 + - - -
526D THR* 1.3 62.8 + - - +
527D THR* 5.2 0.7 - - - +
540D ILE 3.6 1.7 - - - +
541D TYR* 3.6 0.7 - - - -
542D ILE* 2.8 54.0 + - + +
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Residues in contact with THR 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D ARG* 2.7 23.2 + - - -
394D TYR* 4.5 2.1 + - - -
465D ASP* 2.7 18.3 + - - +
467D TRP* 4.0 15.0 + - + +
485D THR* 3.8 25.8 - - + +
486D GLY* 3.2 21.7 - - - -
487D SER* 3.7 6.9 + - - -
524D GLY 4.8 0.2 + - - -
525D HIS* 1.3 75.7 + - - +
527D THR* 1.3 64.4 + - - +
528D CYS* 4.5 4.0 - - - -
539D CYS* 4.6 0.2 - - + -
540D ILE 3.2 5.4 - - - +
541D TYR* 3.4 36.9 - - + -
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Residues in contact with THR 527 (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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167D PHE* 3.9 18.6 - - + +
169D LEU* 4.2 31.2 - - + +
392D ARG* 2.7 29.1 + - - +
467D TRP* 3.8 14.4 - - + -
525D HIS* 5.2 1.2 - - - +
526D THR* 1.3 73.7 + - - +
528D CYS* 1.3 70.8 + - - +
529D PHE* 4.4 1.7 - - + -
538D TYR 4.0 0.3 - - - +
539D CYS* 3.3 0.5 - - - -
540D ILE* 2.8 51.7 + - + +
542D ILE* 6.0 0.2 - - - +
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Residues in contact with CYS 528 (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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127D ILE* 6.1 0.2 - - - +
128D ASN 4.9 0.7 + - - -
131D TYR* 3.3 10.0 + - + -
169D LEU* 5.0 0.5 - - - +
467D TRP* 3.2 55.4 - - + +
469D LEU* 4.2 2.2 - - - -
485D THR* 3.5 20.6 - - - -
526D THR* 4.5 0.9 - - - -
527D THR* 1.3 78.7 - - - +
529D PHE* 1.3 66.3 + - - +
537D VAL* 4.3 4.7 - - + -
538D TYR 3.3 4.7 - - - +
539D CYS* 2.0 44.6 - - - -
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Residues in contact with PHE 529 (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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123D TYR* 3.9 28.7 - + + -
126D GLY 3.8 6.3 - - - +
127D ILE* 4.0 16.2 - - + -
131D TYR* 3.1 14.6 - - - +
169D LEU* 3.9 17.3 - - + -
200D ILE* 4.1 10.1 - - + -
208D PRO* 3.5 33.0 - - + -
210D PHE* 3.8 30.5 - + - -
527D THR* 4.4 2.9 - - + -
528D CYS* 1.3 80.4 - - - +
530D ARG* 1.3 61.9 + - - +
537D VAL* 3.5 2.8 - - - -
538D TYR* 2.9 51.4 + + + +
540D ILE* 4.6 10.5 - - + -
559D ILE* 4.6 2.7 - - + -
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Residues in contact with ARG 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ARG 3.5 6.8 - - - +
123D TYR* 4.0 11.9 - - - +
126D GLY* 2.9 27.4 + - - +
129D GLN* 4.4 9.8 + - - -
130D PHE 4.9 1.2 + - - -
131D TYR* 2.5 72.5 + - + +
132D PHE* 4.6 6.7 - - - -
136D GLU* 5.6 0.2 + - - -
529D PHE* 1.3 75.1 - - - +
531D ASP* 1.3 75.1 + - - +
532D THR* 3.5 17.0 + - + +
535D VAL* 4.1 25.8 + - - +
536D MET 3.5 11.0 - - - +
537D VAL* 4.1 10.7 - - + +
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Residues in contact with ASP 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ARG* 2.5 40.3 + - - +
123D TYR* 4.1 18.3 + - + -
206D GLY 3.8 10.6 - - - +
529D PHE 4.2 0.4 + - - -
530D ARG* 1.3 71.2 - - - +
532D THR* 1.3 52.3 + - - +
533D GLY* 2.7 31.5 + - - -
534D SER* 3.1 19.5 + - - +
535D VAL* 2.7 37.6 + - - -
536D MET 2.7 15.8 + - - +
538D TYR* 4.1 14.8 - - + -
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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
------------------------------------------------------------
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