Contacts of the helix formed by residues 650 - 662 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168P GLU* 3.8 4.8 + - - -
649P VAL* 1.3 72.5 - - - +
651P VAL* 1.3 65.1 + - - +
652P GLU* 2.8 25.6 + - - -
653P LYS* 2.7 55.6 + - - +
654P THR* 3.1 10.0 + - - +
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Residues in contact with VAL 651 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140P PRO* 4.6 7.0 - - + +
141P VAL* 4.2 8.5 - - - +
142P PRO* 3.9 38.6 - - + -
649P VAL 3.1 4.4 + - - +
650P SER* 1.3 71.6 - - - +
652P GLU* 1.3 63.9 + - - +
654P THR* 3.2 5.6 + - - -
655P GLU* 2.8 44.9 + - + +
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Residues in contact with GLU 652 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650P SER* 2.8 29.4 + - - -
651P VAL* 1.3 89.9 + - - +
653P LYS* 1.3 62.0 + - + +
655P GLU* 3.2 15.4 + - - +
656P ARG* 2.8 33.4 + - - +
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Residues in contact with LYS 653 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P GLU* 3.2 43.3 + - + +
171P LEU* 4.0 9.7 - - + +
172P GLU* 3.6 22.2 + - - +
649P VAL* 4.5 7.2 - - + -
650P SER* 2.7 31.6 + - - +
652P GLU* 1.3 78.4 - - + +
654P THR* 1.3 59.8 + - + +
656P ARG* 3.7 7.4 + - - +
657P PHE* 3.2 21.1 + - - +
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Residues in contact with THR 654 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140P PRO* 5.0 0.4 - - - -
141P VAL 2.8 26.3 + - - -
143P LEU* 3.6 37.2 - - + +
171P LEU* 3.8 19.7 - - + -
285P ALA* 5.2 8.3 - - + -
649P VAL* 4.2 9.4 - - + +
650P SER 3.1 10.6 + - - +
651P VAL 3.2 8.3 + - - -
653P LYS* 1.3 72.9 - - - +
655P GLU* 1.3 68.4 + - - +
656P ARG 3.1 0.2 - - - -
657P PHE* 2.9 3.2 + - - +
658P LEU* 2.6 38.5 + - - +
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Residues in contact with GLU 655 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P PRO* 3.6 33.3 - - + +
651P VAL* 2.8 22.1 + - + +
652P GLU* 3.5 14.5 - - - +
654P THR* 1.3 82.4 + - - +
656P ARG* 1.3 60.4 + - - +
658P LEU* 3.6 2.0 + - - +
659P ARG* 3.1 54.8 + - - +
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Residues in contact with ARG 656 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172P GLU* 5.1 16.1 + - - +
652P GLU 2.8 20.4 + - - +
653P LYS* 3.9 7.2 - - - +
655P GLU* 1.3 75.1 - - - +
657P PHE* 1.3 63.5 + - - +
659P ARG* 3.3 30.2 + - - +
660P SER* 3.3 12.0 + - - -
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Residues in contact with PHE 657 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171P LEU* 3.2 48.9 - - + +
174P ALA* 3.8 23.6 - - + -
282P PRO* 3.5 36.8 - - + -
285P ALA* 3.5 18.8 - - + -
286P VAL* 4.4 5.4 - - + -
352P TRP* 3.9 9.2 - + - -
353P TRP* 3.8 6.1 - + - -
653P LYS 3.2 12.5 + - - +
654P THR 2.9 8.4 + - - +
656P ARG* 1.3 79.1 - - - +
658P LEU* 1.3 68.4 + - - +
660P SER* 3.0 25.5 + - - -
661P VAL* 3.3 32.2 + - + +
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Residues in contact with LEU 658 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138P LEU* 4.5 0.9 - - + +
139P GLU 4.2 3.8 - - - -
140P PRO* 3.5 35.7 - - + -
285P ALA* 3.4 24.9 - - + +
286P VAL* 3.9 25.1 - - + -
289P PRO* 4.3 11.2 - - + -
654P THR* 2.6 22.1 + - - +
655P GLU* 3.9 5.2 - - - +
657P PHE* 1.3 78.8 - - + +
659P ARG* 1.3 58.7 + - - +
661P VAL* 3.2 3.6 + - + +
662P MET* 3.0 62.5 + - + +
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Residues in contact with ARG 659 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140P PRO* 5.6 1.6 - - - +
655P GLU* 3.1 51.1 + - - +
656P ARG* 3.4 30.6 - - - +
657P PHE 3.1 0.2 - - - -
658P LEU* 1.3 74.9 - - - +
660P SER* 1.3 57.1 + - - +
661P VAL 3.0 9.2 + - - -
662P MET* 3.6 18.2 + - - +
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Residues in contact with SER 660 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175P GLU* 4.0 13.2 + - - +
350P ALA* 3.8 7.6 - - - +
352P TRP* 3.4 28.1 + - - -
656P ARG 3.3 6.8 + - - -
657P PHE* 3.0 19.4 + - - -
659P ARG* 1.3 78.3 - - - +
661P VAL* 1.3 58.0 + - - +
662P MET 4.7 1.1 - - - +
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Residues in contact with VAL 661 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286P VAL* 4.2 11.0 - - + -
348P GLY 4.5 0.2 - - - +
349P TYR* 3.8 22.2 - - + -
350P ALA* 3.1 29.5 + - - +
352P TRP* 3.3 28.5 - - + -
353P TRP* 3.6 25.4 - - + -
657P PHE* 3.4 32.5 - - + +
658P LEU* 3.5 10.3 - - + +
659P ARG 3.0 0.6 - - - -
660P SER* 1.3 78.9 - - - +
662P MET* 1.3 73.4 + - + +
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Residues in contact with MET 662 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P SER 4.3 4.3 - - - +
138P LEU* 3.5 49.1 - - + +
140P PRO* 5.2 2.7 - - + -
286P VAL* 5.8 0.7 - - + -
348P GLY 4.4 0.5 - - - +
349P TYR* 3.8 21.1 - - + +
658P LEU* 3.0 50.0 + - + +
659P ARG* 3.6 14.9 + - - +
660P SER 4.7 1.2 - - - +
661P VAL* 1.3 88.7 - - + +
663P PRO* 1.3 70.6 - - + +
664P 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