Contacts of the helix formed by residues 638 - 650 (chain D) in PDB entry 5ON2
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 GLY 638 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D TYR* 5.5 0.9 - - - -
7D PRO* 4.0 18.4 - - - -
11D GLU* 4.2 1.6 - - - -
633D MET 3.4 1.6 + - - -
634D VAL* 3.2 20.2 + - - -
637D TYR* 1.3 79.1 - - - +
639D ALA* 1.3 65.4 + - - -
640D ASP 3.4 2.5 - - - -
641D THR* 3.3 6.9 + - - -
642D VAL* 3.3 23.6 + - - +
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Residues in contact with ALA 639 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D GLU* 3.1 22.4 + - - +
114D MET 3.6 22.9 - - - +
115D LEU* 4.1 18.4 - - + +
634D VAL* 4.2 21.8 + - + +
638D GLY* 1.3 69.6 - - - -
640D ASP* 1.3 61.1 + - - +
642D VAL* 3.4 3.8 + - - +
643D ARG* 3.0 34.1 + - - +
767D HIS* 4.3 4.7 - - + -
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Residues in contact with ASP 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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5D TYR* 3.6 11.3 + - - +
11D GLU* 3.2 11.7 + - - +
639D ALA* 1.3 76.0 - - - +
641D THR* 1.3 58.0 + - - +
643D ARG* 3.4 4.5 + - - -
644D LEU* 2.9 26.0 + - - +
670D LEU* 4.0 7.4 - - + -
765D THR* 3.4 34.1 - - + +
766D PRO* 3.6 13.2 - - - +
767D HIS* 2.8 28.3 + - - +
768D ILE* 2.9 37.6 + - - +
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Residues in contact with THR 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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5D TYR* 4.8 4.5 + - - -
637D TYR* 3.6 23.4 + - + -
638D GLY* 3.3 9.1 + - - -
639D ALA 3.3 0.4 - - - -
640D ASP* 1.3 78.4 - - - +
642D VAL* 1.3 56.6 + - + +
645D PHE* 3.1 28.2 + - - +
663D VAL* 3.7 13.7 - - + +
666D ALA* 3.5 5.1 - - - +
667D ASN* 3.3 54.3 + - + +
670D LEU* 3.9 15.6 - - - +
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Residues in contact with VAL 642 (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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50D MET* 4.0 19.7 - - + -
53D VAL* 4.4 12.6 - - + -
115D LEU* 5.1 5.6 - - + -
630D PRO* 5.0 7.2 - - + -
633D MET* 3.6 53.8 - - + +
634D VAL* 4.3 8.1 - - + +
637D TYR* 5.5 1.8 - - + -
638D GLY 3.3 14.6 + - - +
639D ALA* 3.8 6.5 - - - +
640D ASP 3.3 0.2 - - - -
641D THR* 1.3 75.0 - - + +
643D ARG* 1.3 64.5 + - - +
645D PHE* 3.6 4.9 + - - +
646D MET* 3.2 25.9 + - + +
663D VAL* 6.0 0.2 - - - -
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Residues in contact with ARG 643 (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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53D VAL* 5.6 1.1 - - + -
57D THR* 3.8 28.1 + - + +
60D ASP* 2.7 29.7 + - - +
61D VAL* 4.6 2.8 - - - +
64D ARG* 4.0 0.2 - - - +
115D LEU* 3.4 31.0 + - + +
116D GLY 2.9 29.3 + - - -
117D PHE* 3.9 13.6 - - + -
639D ALA 3.0 21.5 + - - +
640D ASP* 3.8 3.4 - - - +
642D VAL* 1.3 77.5 - - - +
644D LEU* 1.3 61.8 + - - +
646D MET* 3.7 1.4 + - - +
647D MET* 3.5 27.5 + - - +
763D PRO 2.8 26.7 + - - -
764D PHE* 3.2 17.9 + - - +
766D PRO* 3.4 23.7 - - - +
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Residues in contact with LEU 644 (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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640D ASP 2.9 19.0 + - - +
641D THR* 4.7 0.2 - - - -
643D ARG* 1.3 74.1 - - - +
645D PHE* 1.3 59.8 - - - +
647D MET 3.7 0.3 + - - -
648D PHE* 3.1 30.9 + - + +
666D ALA* 3.9 29.6 - - + +
669D PHE* 3.7 28.9 - - + -
670D LEU* 4.3 12.1 - - + -
726D ILE* 3.8 37.8 - - + +
730D MET* 5.0 2.5 - - + -
761D LEU* 4.1 12.3 - - + -
764D PHE* 4.0 19.9 + - + -
765D THR* 4.0 5.8 - - + -
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Residues in contact with PHE 645 (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 MET* 4.9 2.5 - - + -
641D THR 3.1 20.1 + - - +
642D VAL* 3.9 3.8 - - - +
644D LEU* 1.3 74.1 - - - +
646D MET* 1.3 63.9 + - + +
648D PHE* 3.3 11.8 + + - -
649D ALA* 3.0 46.5 + - + +
658D TRP* 3.9 26.2 - + - -
659D GLN 3.3 26.0 - - - -
661D SER 4.6 1.6 - - - -
662D GLY* 3.4 35.7 - - - -
663D VAL* 3.5 31.6 - - + -
666D ALA* 4.0 11.6 - - + +
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Residues in contact with MET 646 (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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50D MET* 3.7 45.3 - - + +
53D VAL* 4.2 15.0 - - + -
54D ARG* 4.2 23.1 + - + -
57D THR* 5.2 0.9 - - - +
569D VAL* 5.0 1.6 - - + -
642D VAL* 3.2 19.1 + - + +
643D ARG* 4.1 4.0 - - - +
644D LEU 3.4 0.4 - - - -
645D PHE* 1.3 82.3 - - + +
647D MET* 1.3 78.3 + - + +
649D ALA* 4.0 8.9 + - + +
650D SER 4.3 6.1 + - - +
656D LEU* 3.5 31.8 - - + +
658D TRP* 3.7 20.9 - - + -
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Residues in contact with MET 647 (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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54D ARG* 4.1 12.8 - - + +
57D THR* 3.9 26.2 - - + +
58D ILE* 3.6 36.6 - - + -
61D VAL* 4.5 1.3 - - + -
643D ARG 3.5 16.4 + - - +
645D PHE 3.3 0.4 - - - -
646D MET* 1.3 96.1 - - + +
648D PHE* 1.3 62.5 + - - +
650D SER 3.3 13.4 - - - +
722D PHE* 3.8 25.3 - - + +
723D ASN 3.3 18.4 + - - -
726D ILE* 3.7 19.7 - - + -
764D PHE* 3.9 15.7 - - + -
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Residues in contact with PHE 648 (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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644D LEU* 3.1 21.4 + - + +
645D PHE* 3.3 13.2 + + - +
647D MET* 1.3 77.8 - - - +
649D ALA* 1.3 65.0 + - - +
650D SER 3.5 0.2 - - - -
666D ALA* 6.0 5.2 - - + -
723D ASN* 3.4 31.2 - - + +
726D ILE* 3.6 27.6 - - + +
727D ALA* 4.1 7.9 - - + -
730D MET* 3.9 18.8 - - + -
12E G 3.9 18.8 + - - -
13E G 5.6 1.0 + - - -
22E A 5.6 1.1 - - - -
23E C 3.6 40.4 - - - -
24E A 3.6 26.9 - - - -
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Residues in contact with ALA 649 (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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645D PHE* 3.0 37.1 + - + +
646D MET* 4.2 7.4 - - + +
647D MET 3.4 0.6 - - - -
648D PHE* 1.3 81.4 - - - +
650D SER* 1.3 60.0 + - - +
656D LEU* 4.4 18.6 - - + -
723D ASN* 4.9 0.2 - - - -
12E G 2.7 37.7 + - - +
13E G 3.5 9.5 - - - +
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Residues in contact with SER 650 (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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54D ARG* 3.8 17.2 + - - -
646D MET 4.3 4.7 + - - +
647D MET* 3.3 16.8 + - - +
648D PHE 3.5 0.6 - - - -
649D ALA* 1.3 80.3 - - - +
651D PRO* 1.4 78.7 - - - +
652D ALA* 3.7 1.0 + - - -
654D MET* 3.4 18.2 - - - +
655D THR 4.2 1.6 + - - -
656D LEU* 4.1 20.4 - - - -
722D PHE* 5.6 0.7 + - - +
723D ASN* 4.2 5.4 - - - +
13E G 3.4 17.0 + - - -
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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