Contacts of the helix formed by residues 638 - 645 (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 638 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613Q GLU 4.8 4.0 + - - -
614Q LEU* 5.2 1.6 - - - -
615Q THR* 3.5 10.5 - - - +
618Q ASP* 2.5 37.3 + - - -
636Q ASP 4.4 0.4 + - - -
637Q VAL* 1.3 68.9 - - - +
639Q ALA* 1.3 59.8 + - - +
640Q ASN* 3.3 16.2 - - - -
641Q ILE* 2.8 27.4 + - - +
642Q HIS 2.9 11.1 + - - -
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Residues in contact with ALA 639 (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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637Q VAL 3.2 5.9 + - - -
638Q SER* 1.3 71.3 - - - +
640Q ASN* 1.3 63.4 + - - +
642Q HIS* 3.4 7.3 + - - +
643Q GLU* 3.1 32.4 + - + +
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Residues in contact with ASN 640 (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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602Q VAL* 3.6 21.2 - - + +
603Q ALA* 6.1 0.7 - - + +
604Q SER* 3.1 29.3 + - - +
605Q MET* 5.4 1.4 - - - +
613Q GLU* 6.1 2.8 - - - +
614Q LEU* 4.7 6.9 - - - +
638Q SER* 3.3 18.7 - - - -
639Q ALA* 1.3 76.1 + - - +
641Q ILE* 1.3 69.1 + - - +
643Q GLU* 3.8 23.0 + - - +
644Q VAL* 3.6 14.9 - - - +
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Residues in contact with ILE 641 (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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602Q VAL* 3.9 28.3 - - + -
614Q LEU* 3.5 33.9 - - + -
618Q ASP* 4.3 12.1 - - + +
621Q VAL* 5.5 1.6 - - + -
622Q LEU* 3.8 35.4 - - + -
637Q VAL* 4.1 13.5 - - + -
638Q SER* 2.8 20.9 + - - +
640Q ASN* 1.3 86.6 - - - +
642Q HIS* 1.3 67.3 + - - +
643Q GLU 3.1 1.1 - - - -
644Q VAL* 2.9 21.6 + - + +
645Q LEU* 3.7 9.0 + - + +
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Residues in contact with HIS 642 (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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144Q LYS* 4.2 12.3 - - + -
628Q LEU* 4.2 21.2 - - + +
634Q GLU* 3.3 63.4 + - + +
637Q VAL* 3.7 16.0 - - + +
638Q SER 2.9 11.0 + - - +
639Q ALA* 3.7 11.7 - - - +
641Q ILE* 1.3 76.3 - - - +
643Q GLU* 1.3 58.3 + - - +
645Q LEU* 3.0 8.8 + - - +
646Q MET* 2.8 62.0 + - + +
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Residues in contact with GLU 643 (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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144Q LYS* 6.4 0.2 - - - +
147Q LYS* 2.9 19.1 + - - -
639Q ALA* 3.1 21.0 + - - +
640Q ASN* 3.8 18.9 - - - +
641Q ILE 3.1 0.6 - - - -
642Q HIS* 1.3 77.6 + - - +
644Q VAL* 1.3 56.3 + - - +
646Q MET 3.1 15.3 - - - +
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Residues in contact with VAL 644 (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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147Q LYS* 2.8 26.8 + - - +
540Q SER* 3.1 23.9 - - - -
546Q PHE* 4.7 6.5 - - + -
601Q TYR* 4.0 34.5 - - + +
602Q VAL* 4.2 16.2 - - + -
622Q LEU* 4.7 11.4 - - + -
640Q ASN 3.6 14.1 - - - +
641Q ILE* 2.9 19.5 + - + +
643Q GLU* 1.3 78.8 - - + +
645Q LEU* 1.3 68.8 + - + +
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Residues in contact with LEU 645 (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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146Q ARG* 3.2 32.9 + - - +
147Q LYS* 3.0 30.7 + - - +
540Q SER* 4.2 4.5 - - - +
545Q PRO* 4.3 9.6 - - + -
621Q VAL* 3.5 36.8 - - + +
622Q LEU* 4.6 10.8 - - + -
625Q PRO* 3.8 23.1 - - + -
628Q LEU* 4.2 9.4 - - + -
641Q ILE* 4.1 11.4 - - + +
642Q HIS* 3.0 6.1 + - - +
644Q VAL* 1.3 97.0 - - + +
646Q MET* 1.3 66.4 + - + +
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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