Contacts of the helix formed by residues 680 - 688 (chain D) in PDB entry 1SO2
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 PRO 680 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673D LYS* 4.2 25.5 - - + +
676D ASN* 5.5 2.2 - - + -
678D ASN 3.1 9.6 - - - +
679D PHE* 1.3 91.1 - - + +
681D ILE* 1.3 64.3 + - - +
682D PHE 3.3 2.5 - - - -
683D GLU* 3.1 42.2 + - + +
684D LEU* 3.2 12.1 + - - +
947D LEU* 5.1 6.7 - - + -
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Residues in contact with ILE 681 (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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679D PHE* 2.5 43.4 + - + +
680D PRO* 1.3 70.5 - - - +
682D PHE* 1.3 84.3 + - + +
684D LEU* 3.3 3.0 + - - +
685D VAL* 3.0 25.3 + - - +
695D ILE* 4.2 12.3 - - + -
740D ILE* 3.7 34.3 - - + +
743D THR* 4.1 13.7 - - + -
744D ASP* 3.9 27.8 - - + +
747D HIS* 6.1 0.2 - - + -
947D LEU* 4.5 6.0 - - + +
951D TRP* 4.3 9.4 - - + +
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Residues in contact with PHE 682 (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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680D PRO 3.3 1.2 - - - -
681D ILE* 1.3 89.7 - - + +
683D GLU* 1.3 62.5 + - - +
685D VAL* 3.2 10.8 + - + +
686D GLU* 2.8 28.9 + - - +
740D ILE* 4.2 24.0 - - + -
947D LEU* 4.2 13.9 - - + -
950D LYS* 3.4 54.3 - - + -
951D TRP* 3.7 38.6 - + - -
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Residues in contact with GLU 683 (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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673D LYS* 5.5 8.7 - - - +
680D PRO* 3.1 33.5 + - + +
682D PHE* 1.3 79.0 - - - +
684D LEU* 1.3 50.1 + - - +
686D GLU* 3.0 11.5 + - + +
687D LYS* 2.6 36.8 + - - +
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Residues in contact with LEU 684 (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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670D LEU* 4.4 24.0 - - + -
673D LYS* 5.0 16.3 - - + +
679D PHE* 3.1 39.9 - - + -
680D PRO 3.2 7.7 + - - +
681D ILE 3.4 7.0 - - - +
682D PHE 3.2 0.2 - - - -
683D GLU* 1.3 76.5 - - - +
685D VAL* 1.3 57.4 + - - +
687D LYS* 3.1 8.6 + - + +
688D MET* 2.8 56.2 + - + +
695D ILE* 4.1 22.0 - - + -
699D VAL* 4.3 12.6 - - + -
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Residues in contact with VAL 685 (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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681D ILE 3.0 17.4 + - - +
682D PHE* 3.2 13.2 + - + +
684D LEU* 1.3 77.6 - - - +
686D GLU* 1.3 63.3 + - - +
688D MET* 4.8 1.3 - - - -
689D GLY* 3.6 7.3 + - - +
692D SER* 3.6 34.2 - - - +
695D ILE* 3.6 25.6 - - + -
740D ILE* 3.9 33.2 - - + -
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Residues in contact with GLU 686 (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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682D PHE 2.8 14.5 + - - +
683D GLU* 3.1 17.3 - - + +
685D VAL* 1.3 78.1 - - - +
687D LYS* 1.3 61.6 + - - +
689D GLY* 3.3 12.1 + - - -
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Residues in contact with LYS 687 (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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673D LYS* 4.8 12.6 - - - +
683D GLU 2.6 19.0 + - - +
684D LEU* 3.1 11.0 + - + +
686D GLU* 1.3 71.9 - - - +
688D MET* 1.3 61.0 + - + +
689D GLY* 2.8 12.2 + - - -
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Residues in contact with MET 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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684D LEU* 2.8 47.4 + - + +
685D VAL* 5.2 0.4 - - - -
686D GLU 3.5 0.2 - - - -
687D LYS* 1.3 71.4 - - + +
689D GLY* 1.3 63.8 + - - +
690D GLU 3.2 0.3 + - - -
691D LYS* 2.7 60.8 + - + +
692D SER* 3.5 15.3 - - - -
694D ARG* 3.9 5.4 - - + +
695D ILE* 3.8 35.9 - - - +
698D GLN* 4.5 13.7 - - + +
699D VAL* 6.2 0.4 - - - -
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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