Contacts of the helix formed by residues 687 - 696 (chain D) in PDB entry 2BT4
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 687 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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659D GLU* 2.7 27.0 + - - -
683D TYR* 2.9 31.0 + - - +
686D THR* 1.3 75.1 + - - +
688D VAL* 1.3 62.6 + - - +
689D ALA 3.3 0.3 + - - -
690D ILE* 2.8 29.2 + - - +
691D LEU 3.3 13.0 + - - -
721D TYR* 3.9 14.5 - - - +
722D VAL* 5.1 1.4 - - - +
2406F TRS 3.8 3.1 - - - -
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Residues in contact with VAL 688 (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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686D THR 3.4 2.2 + - - -
687D SER* 1.3 72.9 - - - +
689D ALA* 1.3 56.4 + - - +
691D LEU* 3.3 7.9 + - + +
692D ASP* 2.9 29.3 + - - +
721D TYR* 3.7 34.1 - - + +
1082F ALA* 3.7 20.9 - - + +
1085F HIS* 4.5 7.6 - - + -
1086F THR* 3.7 26.2 - - + +
1116F PHE* 3.8 28.3 - - + -
1117F ARG* 4.1 13.5 - - - +
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Residues in contact with ALA 689 (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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659D GLU* 3.7 9.6 + - - +
663D VAL* 4.0 9.8 - - + +
687D SER* 3.1 0.6 - - - +
688D VAL* 1.3 78.3 - - - +
690D ILE* 1.3 57.3 + - - +
692D ASP 3.4 0.3 + - - -
693D ALA* 3.0 24.4 + - - +
1015F PRO* 4.0 10.3 - - + -
1016F ASN* 3.1 12.5 + - - +
1082F ALA* 3.5 17.2 - - + +
1083F TYR* 3.6 37.6 - - + +
1086F THR* 5.7 0.4 - - - +
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Residues in contact with ILE 690 (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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659D GLU* 4.3 6.7 - - + +
662D LEU* 3.9 30.5 - - + -
663D VAL* 4.1 16.2 - - + -
666D ILE* 3.9 17.0 - - + -
678D ILE* 4.2 10.3 - - + -
680D PRO* 5.2 4.3 - - + -
683D TYR* 3.8 26.9 - - + -
687D SER* 2.8 23.3 + - - +
689D ALA* 1.3 72.3 - - - +
691D LEU* 1.3 68.4 + - - +
693D ALA* 3.2 6.7 + - - +
694D LEU* 3.0 28.6 + - + +
722D VAL* 4.0 19.5 - - + -
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Residues in contact with LEU 691 (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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687D SER 3.3 10.1 + - - +
688D VAL* 3.3 9.2 + - + +
690D ILE* 1.3 79.1 - - - +
692D ASP* 1.3 57.4 + - - +
694D LEU* 3.1 9.9 + - - +
695D ASN* 2.8 45.1 + - - +
721D TYR* 3.4 40.2 - - + +
722D VAL* 4.8 3.0 - - - +
724D GLN* 4.0 14.6 - - + +
725D ARG* 3.6 28.7 - - + +
1116F PHE* 3.7 31.0 - - + -
1117F ARG* 4.2 5.2 - - - +
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Residues in contact with ASP 692 (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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688D VAL 2.9 20.3 + - - +
689D ALA 4.3 0.4 - - - -
691D LEU* 1.3 72.0 - - - +
693D ALA* 1.3 62.1 + - - +
695D ASN* 3.2 18.2 + - - +
696D THR* 3.3 17.5 + - - +
1016F ASN* 3.5 21.4 + - + +
1081F ALA* 5.3 0.2 - - - +
1082F ALA* 3.3 12.9 - - - +
1117F ARG* 2.8 34.1 + - - -
1160F CA2 2.4 41.7 + - + +
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Residues in contact with ALA 693 (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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663D VAL* 3.9 14.6 - - + -
666D ILE* 3.7 26.3 - - + +
667D HIS* 4.1 2.7 - - - +
689D ALA 3.0 13.4 + - - +
690D ILE* 3.6 7.9 - - - +
691D LEU 3.2 0.2 - - - -
692D ASP* 1.3 77.1 - - - +
694D LEU* 1.3 61.6 + - - +
696D THR* 2.7 24.9 + - - -
697D CYS* 3.7 7.3 - - - -
1016F ASN* 3.1 23.0 + - - +
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Residues in contact with LEU 694 (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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666D ILE* 3.9 17.7 - - + -
676D ILE* 3.8 33.0 - - + -
678D ILE* 4.6 6.7 - - + -
690D ILE* 3.0 28.0 + - + +
691D LEU* 3.6 6.3 - - - +
693D ALA* 1.3 76.6 - - - +
695D ASN* 1.3 63.4 + - - +
697D CYS* 2.9 24.5 + - - +
702D VAL* 4.1 24.9 - - + -
722D VAL* 3.8 35.2 - - + +
725D ARG* 3.4 26.7 + - + -
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Residues in contact with ASN 695 (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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691D LEU* 2.8 34.6 + - - +
692D ASP* 3.3 21.2 + - - +
693D ALA 3.1 0.2 - - - -
694D LEU* 1.3 78.3 - - - +
696D THR* 1.3 58.1 + - - +
697D CYS 3.1 1.7 + - - -
698D ASP* 4.1 3.6 + - - +
724D GLN 5.3 0.7 - - - +
725D ARG* 3.5 28.8 + - - +
1023F ARG* 3.0 35.8 + - - +
1117F ARG* 4.1 7.3 - - - +
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Residues in contact with THR 696 (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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667D HIS* 4.1 4.3 - - - -
670D ARG* 2.7 41.9 + - - -
692D ASP 3.4 14.6 - - - +
693D ALA* 2.7 19.8 + - - +
695D ASN* 1.3 76.0 - - + +
697D CYS* 1.3 55.3 + - - +
698D ASP* 3.0 18.7 + - - +
1016F ASN* 4.6 6.7 - - + +
1019F LEU* 3.7 20.0 - - + +
1023F ARG* 3.5 20.7 - - - +
1160F CA2 4.3 19.7 - - + -
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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