Contacts of the helix formed by residues 630 - 641 (chain D) in PDB entry 5Y7K
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 SER 630 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547D TYR* 4.4 9.6 + - - -
629D TRP* 1.3 78.7 - - - +
631D TYR* 1.3 71.6 + - - -
633D GLY* 2.9 12.1 + - - -
634D TYR 3.2 8.5 + - - -
653D VAL 2.9 12.1 + - - -
654D ALA 3.2 15.3 - - - -
655D PRO* 3.6 7.0 - - - +
656D VAL 4.1 1.7 + - - -
740D HIS* 3.0 20.4 + - - -
801D 8VU 2.9 38.4 - - - -
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Residues in contact with TYR 631 (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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547D TYR* 3.1 39.2 - - + +
548D ALA 3.4 11.0 - - - -
549D GLY* 3.6 7.2 - - - -
550D PRO* 3.6 20.2 - - + +
598D LEU* 3.6 18.8 - - + +
602D GLU* 2.5 40.8 + - - -
629D TRP 3.1 0.8 + - - -
630D SER* 1.3 81.4 + - - +
632D GLY* 1.3 57.2 + - - +
634D TYR* 3.1 11.4 + + - +
635D VAL* 3.0 32.8 + - + +
656D VAL* 5.6 0.2 - - - -
659D TRP* 3.3 27.8 - + - -
666D TYR* 3.6 7.6 - - - -
801D 8VU 2.9 30.6 - - - -
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Residues in contact with GLY 632 (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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546D VAL* 3.3 28.8 - - - +
547D TYR* 3.6 13.8 + - - +
628D GLY* 3.5 7.6 - - - -
629D TRP 2.8 10.8 + - - -
631D TYR* 1.3 78.8 - - - +
633D GLY* 1.3 56.0 + - - +
635D VAL* 4.4 0.7 - - - -
636D THR* 2.8 34.1 + - - -
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Residues in contact with GLY 633 (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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628D GLY 3.3 22.2 - - - -
629D TRP 3.5 0.6 - - - -
630D SER 2.9 9.4 + - - -
632D GLY* 1.3 75.0 - - - +
634D TYR* 1.3 62.0 + - - +
636D THR* 3.7 2.5 - - - -
637D SER* 2.9 30.1 + - - -
652D ALA* 3.9 8.8 - - - +
653D VAL 4.4 2.0 - - - -
655D PRO* 3.4 17.7 - - - +
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Residues in contact with TYR 634 (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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599D GLY* 3.4 34.0 - - - -
602D GLU* 4.5 5.4 - - - -
603D VAL* 5.1 0.2 - - + -
630D SER 3.2 5.9 + - - +
631D TYR* 3.1 14.8 + + - +
633D GLY* 1.3 75.6 - - - +
635D VAL* 1.3 73.0 + - + +
637D SER* 3.2 4.1 + - - -
638D MET* 2.9 47.9 + - + +
655D PRO* 3.6 2.4 - - - +
656D VAL* 3.0 49.1 - - + +
657D SER 4.1 4.9 - - - -
659D TRP* 3.5 35.4 + + + -
686D SER* 2.8 35.5 + - - -
688D VAL* 3.8 7.0 - - + -
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Residues in contact with VAL 635 (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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546D VAL* 4.4 10.3 - - + -
547D TYR 3.7 8.7 - - - +
548D ALA* 4.2 7.6 - - + -
602D GLU* 4.0 9.2 - - + +
603D VAL* 4.3 14.1 - - + -
606D GLN* 4.0 26.5 - - + -
626D ILE* 5.1 0.2 - - + -
631D TYR* 3.0 45.2 + - + +
632D GLY 3.9 3.6 - - - +
634D TYR* 1.3 78.5 - - + +
636D THR* 1.3 58.0 + - - +
638D MET* 3.2 5.8 + - - +
639D VAL* 2.8 42.8 + - + +
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Residues in contact with THR 636 (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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546D VAL* 3.2 16.1 - - - +
626D ILE* 3.5 32.9 - - + +
627D TRP 3.3 11.4 - - - -
632D GLY 2.8 24.3 + - - -
633D GLY 3.7 5.2 - - - -
635D VAL* 1.3 77.0 - - - +
637D SER* 1.3 56.8 + - - +
639D VAL* 3.2 2.3 + - - +
640D LEU* 2.8 45.6 + - + +
651D ILE 3.5 24.9 - - - +
652D ALA* 4.8 1.8 - - + +
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Residues in contact with SER 637 (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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633D GLY 2.9 19.1 + - - -
634D TYR* 3.7 4.3 - - - -
636D THR* 1.3 76.2 - - - +
638D MET* 1.3 63.9 + - - +
640D LEU* 3.3 0.6 + - - -
641D GLY* 3.0 19.2 + - - -
652D ALA* 3.5 6.1 - - - +
655D PRO* 4.3 4.2 - - - +
688D VAL* 4.1 21.5 - - - +
691D ARG* 5.3 0.3 - - - +
695D PHE* 3.2 23.5 - - - -
700D TYR* 2.9 31.3 + - - -
719D ILE* 4.7 1.0 - - - +
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Residues in contact with MET 638 (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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599D GLY 4.0 10.3 - - - +
603D VAL* 3.8 18.4 - - + -
634D TYR* 2.9 51.0 + - + +
635D VAL 3.7 3.4 - - - +
637D SER* 1.3 75.3 - - - +
639D VAL* 1.3 64.2 + - - +
641D GLY 3.3 1.2 + - - -
642D SER* 3.3 8.0 + - - -
686D SER* 3.5 25.4 - - - +
687D THR 3.6 17.0 - - - +
688D VAL* 3.6 18.4 - - + -
691D ARG* 2.8 57.0 + - - +
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Residues in contact with VAL 639 (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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603D VAL* 3.5 25.4 - - + +
606D GLN* 4.4 3.6 - - + -
607D ILE* 3.8 15.9 - - + -
626D ILE* 3.9 23.1 - - + -
635D VAL* 2.8 27.4 + - + +
636D THR 3.5 4.3 - - - +
638D MET* 1.3 75.1 - - - +
640D LEU* 1.3 62.6 + - - +
641D GLY 3.0 0.5 + - - -
642D SER* 2.7 25.6 + - - -
643D GLY 4.6 0.3 + - - -
644D SER* 4.5 3.0 + - - +
647D PHE* 3.4 40.5 - - + -
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Residues in contact with LEU 640 (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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626D ILE* 4.0 13.0 - - + -
636D THR* 2.8 28.6 + - + +
637D SER 3.3 4.5 + - - +
639D VAL* 1.3 72.0 - - - +
641D GLY* 1.3 56.4 + - - +
642D SER 3.4 1.1 + - - -
643D GLY 4.7 2.1 + - - -
647D PHE* 4.1 10.3 - - + -
649D CYS 3.7 23.8 - - - +
650D GLY* 3.5 22.2 - - - +
694D ASN* 4.0 9.2 - - - +
695D PHE* 3.9 12.0 - - + -
698D VAL* 3.8 45.5 - - + +
699D GLU 4.7 0.7 - - - +
700D TYR* 3.4 33.2 - - + -
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Residues in contact with GLY 641 (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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637D SER 3.0 12.6 + - - -
638D MET 3.6 4.7 - - - -
639D VAL 3.0 0.6 + - - -
640D LEU* 1.3 75.5 - - - +
642D SER* 1.3 55.4 + - - +
643D GLY 3.4 1.8 - - - -
691D ARG* 3.2 20.5 - - - +
694D ASN* 2.8 36.9 + - - -
695D PHE* 3.8 19.1 - - - -
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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