Contacts of the helix formed by residues 650 - 662 (chain Q) in PDB entry 1HI0
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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168Q GLU* 3.8 5.5 + - - -
649Q VAL* 1.3 72.9 - - - +
651Q VAL* 1.3 65.8 + - - +
652Q GLU* 2.8 24.7 + - - -
653Q LYS* 2.7 55.5 + - - +
654Q THR* 3.1 10.2 + - - +
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Residues in contact with VAL 651 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Q PRO* 4.6 7.2 - - + +
141Q VAL* 4.2 8.5 - - - +
142Q PRO* 3.9 38.1 - - + -
649Q VAL 3.1 3.6 + - - -
650Q SER* 1.3 70.9 - - - +
652Q GLU* 1.3 63.4 + - - +
654Q THR* 3.2 7.0 + - - +
655Q GLU* 2.8 45.2 + - + +
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Residues in contact with GLU 652 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650Q SER* 2.8 29.8 + - - -
651Q VAL* 1.3 91.6 + - - +
653Q LYS* 1.3 62.3 + - + +
655Q GLU* 3.2 14.5 + - - +
656Q ARG* 2.8 33.9 + - - +
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Residues in contact with LYS 653 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168Q GLU* 3.2 43.1 + - + +
171Q LEU* 4.0 9.0 - - + +
172Q GLU* 3.6 22.0 + - - +
649Q VAL* 4.5 7.2 - - + -
650Q SER* 2.7 33.0 + - - +
652Q GLU* 1.3 77.7 - - + +
654Q THR* 1.3 59.5 + - - +
656Q ARG* 3.7 7.5 + - - +
657Q PHE* 3.2 21.7 + - - +
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Residues in contact with THR 654 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Q PRO* 5.0 0.4 - - - -
141Q VAL 2.8 25.7 + - - -
143Q LEU* 3.6 37.5 - - + +
171Q LEU* 3.8 20.4 - - + -
285Q ALA* 5.2 9.2 - - + -
649Q VAL* 4.2 8.3 - - + +
650Q SER 3.1 12.0 + - - +
651Q VAL 3.2 8.3 + - - -
653Q LYS* 1.3 74.5 - - - +
655Q GLU* 1.3 67.3 + - - +
657Q PHE* 2.9 2.6 + - - +
658Q LEU* 2.6 37.9 + - - +
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Residues in contact with GLU 655 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Q PRO* 3.6 34.0 - - + +
651Q VAL* 2.8 21.0 + - + +
652Q GLU* 3.5 14.5 - - - +
654Q THR* 1.3 82.2 + - - +
656Q ARG* 1.3 61.4 + - - +
658Q LEU* 3.9 1.6 - - - +
659Q ARG* 3.1 53.8 + - - +
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Residues in contact with ARG 656 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172Q GLU* 5.1 15.9 + - - +
652Q GLU 2.8 20.8 + - - +
653Q LYS* 3.9 7.4 - - - +
655Q GLU* 1.3 74.7 - - - +
657Q PHE* 1.3 63.2 + - - +
659Q ARG* 3.3 30.0 + - - +
660Q SER* 3.3 11.8 + - - -
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Residues in contact with PHE 657 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171Q LEU* 3.2 46.7 - - + +
174Q ALA* 3.8 23.6 - - + -
282Q PRO* 3.5 28.0 - - + -
285Q ALA* 3.5 28.0 - - + -
286Q VAL* 4.4 5.2 - - + -
352Q TRP* 3.9 9.4 - + - -
353Q TRP* 3.8 5.4 - + - -
653Q LYS 3.2 13.0 + - - +
654Q THR 2.9 9.1 + - - +
656Q ARG* 1.3 79.7 - - - +
658Q LEU* 1.3 66.3 + - - +
660Q SER* 3.0 25.8 + - - -
661Q VAL* 3.3 33.4 + - + +
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Residues in contact with LEU 658 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q LEU* 4.5 1.1 - - + +
139Q GLU 4.2 2.9 - - - -
140Q PRO* 3.5 36.3 - - + -
285Q ALA* 3.4 24.7 - - + +
286Q VAL* 3.9 24.9 - - + -
289Q PRO* 4.3 11.2 - - + -
654Q THR* 2.6 21.7 + - - +
655Q GLU* 3.9 5.2 - - - +
657Q PHE* 1.3 79.4 - - + +
659Q ARG* 1.3 56.7 + - - +
661Q VAL* 3.2 3.5 + - + +
662Q MET* 3.0 61.4 + - + +
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Residues in contact with ARG 659 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Q PRO* 5.6 1.4 - - - +
655Q GLU* 3.1 51.0 + - - +
656Q ARG* 3.4 30.6 - - - +
657Q PHE 3.1 0.4 - - - -
658Q LEU* 1.3 74.2 - - - +
660Q SER* 1.3 56.7 + - - +
661Q VAL 3.0 8.7 + - - -
662Q MET* 3.6 18.5 - - - +
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Residues in contact with SER 660 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175Q GLU* 4.0 12.6 + - - +
350Q ALA* 3.8 7.6 - - - +
352Q TRP* 3.4 28.8 + - - -
656Q ARG 3.3 6.6 + - - -
657Q PHE* 3.0 19.4 + - - -
659Q ARG* 1.3 77.2 - - - +
661Q VAL* 1.3 57.3 + - - +
662Q MET 4.7 0.8 - - - +
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Residues in contact with VAL 661 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286Q VAL* 4.2 10.5 - - + -
349Q TYR* 3.8 22.9 - - + -
350Q ALA* 3.1 29.2 + - - +
352Q TRP* 3.3 28.3 - - + -
353Q TRP* 3.6 25.8 - - + -
657Q PHE* 3.4 32.5 - - + +
658Q LEU* 3.5 9.9 - - + +
659Q ARG 3.0 1.0 - - - -
660Q SER* 1.3 79.1 - - - +
662Q MET* 1.3 71.9 + - + +
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Residues in contact with MET 662 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Q SER 4.3 4.3 - - - +
138Q LEU* 3.5 48.7 - - + +
140Q PRO* 5.2 2.7 - - + -
286Q VAL* 5.8 0.2 - - + -
348Q GLY 4.4 0.5 - - - +
349Q TYR* 3.8 21.1 - - + +
658Q LEU* 3.0 49.8 + - + +
659Q ARG* 3.6 14.3 + - - +
660Q SER 4.7 1.0 - - - -
661Q VAL* 1.3 89.3 - - + +
663Q PRO* 1.3 70.6 - - + +
664Q ARG* 4.0 20.1 + - - +
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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