Contacts of the helix formed by residues 650 - 662 (chain C) in PDB entry 1HHS
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 650 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C PRO* 4.9 0.4 - - - -
168C GLU* 4.5 4.5 + - - -
648C GLY 4.1 1.4 + - - -
649C VAL* 1.3 76.0 - - - +
651C VAL* 1.3 62.2 + - - +
652C GLU* 2.8 33.7 + - - +
653C LYS* 2.7 49.0 + - - +
654C THR* 3.2 12.1 + - - +
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Residues in contact with VAL 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PRO* 4.1 11.4 - - + +
141C VAL* 3.9 28.3 - - - +
142C PRO* 4.1 18.5 - - + +
649C VAL 3.5 2.0 + - - -
650C SER* 1.3 71.8 - - - +
652C GLU* 1.3 70.7 + - + +
653C LYS 3.3 0.2 - - - -
654C THR* 3.5 9.9 - - - +
655C GLU* 2.7 43.5 + - + +
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Residues in contact with GLU 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650C SER* 2.8 23.2 + - - +
651C VAL* 1.3 102.4 + - + +
653C LYS* 1.3 63.0 + - + +
655C GLU* 3.8 10.2 - - - +
656C ARG* 3.3 22.5 + - - +
659C ARG* 5.6 0.3 + - - -
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Residues in contact with LYS 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C GLU* 3.7 41.0 + - + +
171C LEU* 4.3 9.6 - - + +
172C GLU* 4.6 14.4 + - + +
649C VAL* 4.2 10.1 - - + -
650C SER* 2.7 29.1 + - - +
652C GLU* 1.3 80.9 - - + +
654C THR* 1.3 61.2 + - + +
656C ARG* 3.6 6.3 + - - +
657C PHE* 3.2 20.6 + - - +
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Residues in contact with THR 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PRO* 4.4 1.4 - - - +
141C VAL 2.8 24.4 + - - +
142C PRO* 4.3 0.4 - - + -
143C LEU* 3.8 31.9 - - + +
171C LEU* 4.0 18.6 - - + -
285C ALA* 5.1 10.5 - - + -
649C VAL* 4.3 5.2 - - + -
650C SER 3.2 13.4 + - - +
651C VAL* 3.4 11.4 + - - +
653C LYS* 1.3 75.8 - - - +
655C GLU* 1.3 63.2 + - - +
657C PHE* 3.1 7.0 + - - +
658C LEU* 2.8 35.6 + - - +
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Residues in contact with GLU 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PRO* 3.8 31.1 - - + +
651C VAL* 2.7 31.4 + - + +
652C GLU* 3.8 10.1 - - - +
654C THR* 1.3 73.6 + - - +
656C ARG* 1.3 61.0 + - - +
658C LEU* 3.4 1.6 + - - +
659C ARG* 2.9 60.1 + - - +
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Residues in contact with ARG 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLU* 5.5 9.7 - - - +
652C GLU 3.3 14.5 + - - +
653C LYS* 3.9 5.8 - - - +
654C THR 3.2 0.4 - - - -
655C GLU* 1.3 77.5 - - - +
657C PHE* 1.3 66.7 + - - +
659C ARG* 3.5 22.4 + - - +
660C SER* 3.4 18.4 + - - -
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Residues in contact with PHE 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LEU* 3.3 36.1 - - + +
174C ALA* 3.8 23.3 - - + -
282C PRO* 3.5 38.1 - - + -
285C ALA* 3.6 23.8 - - + -
286C VAL* 4.5 4.3 - - + -
352C TRP* 3.8 12.6 - + - -
353C TRP* 3.8 7.6 - + - -
653C LYS 3.2 15.5 + - - +
654C THR* 3.1 9.8 + - - +
656C ARG* 1.3 78.2 - - - +
658C LEU* 1.3 67.6 + - + +
660C SER* 2.6 27.9 + - - -
661C VAL* 3.3 26.5 + - + +
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Residues in contact with LEU 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 4.9 1.1 - - + -
139C GLU 4.1 2.9 - - - -
140C PRO* 3.5 40.4 - - + -
285C ALA* 3.1 30.7 - - + +
286C VAL* 4.0 17.7 - - + -
289C PRO* 4.2 11.2 - - + -
654C THR* 2.8 20.6 + - - +
655C GLU 3.8 4.0 - - - +
657C PHE* 1.3 82.7 - - + +
659C ARG* 1.3 61.4 + - - +
661C VAL* 3.0 4.1 + - + +
662C MET* 3.0 60.1 + - + +
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Residues in contact with ARG 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PRO* 5.7 0.2 - - - +
655C GLU* 2.9 56.3 + - - +
656C ARG* 3.7 26.4 - - + +
657C PHE 3.3 0.2 - - - -
658C LEU* 1.3 77.0 - - - +
660C SER* 1.3 61.2 + - - +
661C VAL 3.4 0.5 + - - -
662C MET* 3.8 15.1 - - - +
664C ARG 5.5 4.3 - - - +
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Residues in contact with SER 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C GLU* 4.8 7.6 - - - -
350C ALA* 3.6 8.5 - - - +
352C TRP* 3.5 31.6 + - - -
656C ARG 3.4 8.3 + - - -
657C PHE* 2.6 23.8 + - - -
659C ARG* 1.3 80.0 - - - +
661C VAL* 1.3 57.5 + - - +
662C MET 4.7 0.8 - - - +
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Residues in contact with VAL 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C VAL* 4.2 8.5 - - + -
349C TYR* 3.5 26.3 - - + -
350C ALA* 2.9 30.8 + - - +
352C TRP* 3.6 22.9 - - + -
353C TRP* 3.7 28.0 - - + -
657C PHE* 3.4 38.1 - - + +
658C LEU* 3.0 8.3 + - + +
660C SER* 1.3 78.7 - - - +
662C MET* 1.3 69.1 + - + +
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Residues in contact with MET 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C SER 3.9 13.2 - - - +
138C LEU* 3.4 50.0 - - + +
140C PRO* 5.5 1.3 - - + -
286C VAL* 5.9 1.1 - - + -
348C GLY 4.5 1.1 - - - +
349C TYR* 3.9 21.8 - - + +
658C LEU* 3.0 51.6 + - + +
659C ARG* 3.8 12.1 - - - +
660C SER 4.7 0.9 - - - +
661C VAL* 1.3 85.2 - - + +
663C PRO* 1.3 74.5 - - + +
664C ARG* 3.6 2.4 + - - +
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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