Contacts of the helix formed by residues 657 - 669 (chain D) in PDB entry 2JJD
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 ASP 657 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398D GLY 4.7 3.5 - - - +
400D THR* 2.7 32.2 + - - -
401D GLU* 3.5 20.1 + - + +
646D ILE* 4.7 4.6 - - - +
649D ARG* 3.8 23.1 + - - +
656D LEU* 1.3 72.3 - - - +
658D VAL* 1.3 61.9 + - - +
659D PHE 3.4 3.1 + - - -
660D GLN* 3.0 40.2 + - + +
661D ALA* 3.1 23.3 + - - +
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Residues in contact with VAL 658 (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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400D THR 4.7 1.2 + - - -
646D ILE* 4.1 28.7 - - + -
656D LEU* 3.9 16.1 + - + +
657D ASP* 1.3 70.9 - - - +
659D PHE* 1.3 66.1 + - - +
661D ALA* 3.2 2.1 + - - +
662D VAL* 3.0 25.2 + - + +
679D TYR* 3.8 20.9 - - + -
682D CYS* 4.1 20.0 - - + -
683D TYR* 3.7 45.1 + - + +
686D VAL* 4.7 7.0 - - + -
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Residues in contact with PHE 659 (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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397D TYR* 3.5 50.0 - + + -
400D THR* 3.8 24.0 - - + +
429D GLU* 3.7 28.5 - - + +
432D LYS* 4.1 7.2 - - + -
433D LEU* 3.4 34.4 - - + +
657D ASP* 3.3 6.8 + - - +
658D VAL* 1.3 80.2 - - - +
660D GLN* 1.3 76.2 + - + +
662D VAL 4.0 0.2 - - - -
663D LYS* 3.0 35.2 + - + +
679D TYR* 3.3 23.9 + - - +
683D TYR* 4.3 2.2 + - - +
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Residues in contact with GLN 660 (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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311D ILE* 4.0 21.1 - - + +
393D GLU* 3.1 27.3 + - - +
397D TYR* 3.8 23.6 - - - +
398D GLY 5.7 1.9 + - - +
400D THR* 4.4 1.8 + - - +
657D ASP* 3.0 32.1 + - + +
659D PHE* 1.3 85.6 - - + +
661D ALA* 1.3 60.9 + - - +
663D LYS* 3.6 17.6 - - - +
664D SER* 2.9 31.2 + - - -
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Residues in contact with ALA 661 (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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642D ALA* 4.9 4.0 - - - +
645D ASN* 5.7 4.8 + - + -
646D ILE* 3.6 29.4 - - + +
657D ASP 3.1 20.7 + - - +
658D VAL 3.5 5.2 - - - +
660D GLN* 1.3 78.6 - - - +
662D VAL* 1.3 57.3 + - - +
664D SER* 3.5 6.1 + - - -
665D LEU* 3.2 28.7 + - - +
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Residues in contact with VAL 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D LEU* 3.3 26.7 - - + -
642D ALA* 4.2 13.2 - - + -
646D ILE* 5.2 0.2 - - + -
658D VAL* 3.0 25.1 + - + +
661D ALA* 1.3 74.4 - - + +
663D LYS* 1.3 66.8 + - - +
664D SER 3.1 0.9 - - - -
665D LEU* 3.1 8.2 + - - +
666D ARG* 2.9 30.9 + - + +
673D VAL* 3.5 42.8 - - + +
679D TYR* 4.2 13.5 - - + -
682D CYS* 5.0 2.7 - - - -
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Residues in contact with LYS 663 (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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393D GLU* 2.7 35.9 + - - -
397D TYR* 3.2 23.0 + - + -
433D LEU* 3.4 16.6 - - + +
436D VAL* 5.3 8.1 - - + -
659D PHE* 3.0 33.5 + - + +
660D GLN* 3.6 20.2 - - - +
662D VAL* 1.3 77.0 - - - +
664D SER* 1.3 62.4 + - - +
666D ARG* 3.1 15.5 + - - +
667D LEU* 3.2 36.0 + - + +
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Residues in contact with SER 664 (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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660D GLN* 2.9 18.7 + - - -
661D ALA* 3.6 8.3 - - - -
662D VAL 3.1 0.2 - - - -
663D LYS* 1.3 76.9 - - - +
665D LEU* 1.3 62.4 + - - +
667D LEU* 3.5 13.7 + - - +
668D GLN* 3.3 30.2 + - - +
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Residues in contact with LEU 665 (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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487D ILE* 3.5 24.2 - - + -
638D GLY* 3.5 25.1 - - - +
641D ILE* 3.7 11.0 - - + -
642D ALA* 3.5 25.4 - - + -
645D ASN* 5.1 4.5 - - - +
661D ALA 3.2 12.7 + - - +
662D VAL* 3.1 13.8 + - + +
664D SER* 1.3 78.8 - - - +
666D ARG* 1.3 56.6 + - - +
668D GLN* 3.0 21.9 + - - +
669D ARG 3.1 13.7 + - - +
672D MET* 3.1 41.4 - - + +
673D VAL* 4.6 4.3 - - + -
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Residues in contact with ARG 666 (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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430D PHE* 3.7 28.9 - - - -
433D LEU* 3.9 28.9 + - + +
434D THR* 4.0 15.6 + - - +
436D VAL* 4.4 20.2 + - + +
438D ILE* 6.3 0.2 - - - +
463D TYR* 3.9 11.6 + - - -
662D VAL* 2.9 28.6 + - + +
663D LYS* 3.1 11.4 + - - +
665D LEU* 1.3 75.8 - - - +
667D LEU* 1.3 62.9 + - - +
668D GLN 3.2 0.4 + - - -
669D ARG 3.6 18.6 + - - +
670D PRO* 4.4 1.7 - - - +
671D HIS* 4.2 25.2 + - - +
672D MET* 4.3 11.9 - - + +
673D VAL* 2.7 29.7 + - - +
674D GLN* 4.3 4.4 + - - +
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Residues in contact with LEU 667 (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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309D THR* 4.8 18.8 - - - -
436D VAL* 4.6 17.0 - - + -
437D ARG 5.4 6.1 - - - +
463D TYR* 3.6 10.3 - - - -
465D PHE* 3.5 17.5 - - - -
663D LYS* 3.2 35.5 + - + +
664D SER* 3.5 8.5 + - - +
665D LEU 3.2 0.4 - - - -
666D ARG* 1.3 79.9 - - - +
668D GLN* 1.3 62.3 + - + +
669D ARG 3.5 0.2 - - - -
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Residues in contact with GLN 668 (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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463D TYR* 3.6 6.8 - - - -
465D PHE* 4.1 5.1 - - + -
466D ASN* 2.9 39.6 + - - +
485D SER* 4.0 3.3 + - - -
486D PHE 3.7 4.7 - - - +
487D ILE* 3.4 26.6 - - + +
488D ASP* 3.1 50.0 + - - +
664D SER* 3.3 26.7 + - - +
665D LEU* 3.0 9.6 + - - +
667D LEU* 1.3 83.0 - - + +
669D ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D ILE* 3.7 15.9 + - - +
461D ILE 4.9 1.1 - - - +
462D PRO* 4.1 7.3 - - - +
463D TYR* 3.7 1.9 - - - -
483D ASN* 3.1 32.7 + - - -
484D ALA 3.8 2.2 - - - +
485D SER* 3.2 37.6 + - - +
487D ILE* 4.5 2.7 - - + -
498D ALA* 3.5 21.2 + - - -
500D GLN 4.5 0.8 - - - +
632D ALA 3.8 2.4 + - - -
633D GLY* 2.8 42.5 + - - -
634D ALA* 4.0 4.2 - - - +
665D LEU 3.1 6.3 + - - +
666D ARG* 3.6 9.1 - - - +
667D LEU 3.5 1.6 - - - -
668D GLN* 1.3 83.4 - - - +
670D PRO* 1.3 82.5 - - + +
671D HIS 3.6 1.2 + - - -
672D MET* 3.0 40.5 - - + +
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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