Contacts of the helix formed by residues 634 - 648 (chain H) in PDB entry 5G04
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 HIS 634 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479H TYR* 4.7 11.0 - - - -
601H ALA* 4.1 12.8 - - + +
602H TYR* 3.3 29.3 - + - -
605H THR* 2.8 29.3 + - - -
627H ALA* 4.9 2.5 - - - +
628H ILE* 4.5 0.3 - - - +
631H ASN* 3.3 38.4 + - + +
632H PRO 3.5 0.6 - - - -
633H ARG* 1.3 75.5 - - - +
635H TYR* 1.3 64.7 + + - +
636H ASN* 3.1 36.5 + - + -
637H ALA* 3.3 18.6 + - - +
638H TRP* 3.9 6.5 + - - -
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Residues in contact with TYR 635 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479H TYR* 3.5 31.0 - + - -
510H PHE* 5.0 4.2 - - - -
511H GLU* 4.4 14.0 - - + +
633H ARG 3.5 2.6 + - - -
634H HIS* 1.3 72.3 - + - +
636H ASN* 1.3 90.0 + - - +
638H TRP* 2.6 33.6 + - - +
639H TYR* 2.8 13.5 + - + -
661H ALA* 3.9 22.9 - - + +
664H ILE* 4.1 11.2 - - + -
665H ASN* 3.5 29.2 + - + -
671H LEU* 3.9 22.9 - - + -
183L ILE* 3.2 35.9 - - + +
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Residues in contact with ASN 636 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510H PHE* 5.2 5.7 - - - -
538H ILE* 5.6 0.3 - - - +
602H TYR* 3.6 11.1 - - - -
605H THR* 3.5 8.1 - - + -
609H HIS* 4.1 5.4 + - - -
634H HIS* 3.1 34.0 + - + -
635H TYR* 1.3 113.4 + - - +
637H ALA* 1.3 58.1 + - - +
639H TYR* 3.5 11.4 - - - +
640H GLY* 3.0 22.0 + - - -
183L ILE* 4.3 8.7 - - - +
184L ARG 2.7 33.9 + - - +
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Residues in contact with ALA 637 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605H THR* 4.2 4.8 - - - +
624H PHE* 3.5 19.1 - - + +
627H ALA* 3.2 34.8 - - + -
628H ILE* 3.6 17.9 - - + +
634H HIS* 3.3 8.6 + - - +
635H TYR 3.0 0.6 - - - -
636H ASN* 1.3 76.4 - - - +
638H TRP* 1.3 56.3 + - - +
640H GLY* 3.0 2.3 + - - -
641H LEU* 2.8 36.0 + - - +
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Residues in contact with TRP 638 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628H ILE* 3.6 33.3 - - + +
632H PRO 2.8 23.8 + - - -
634H HIS 4.0 9.9 - - - -
635H TYR* 2.6 17.0 + - - +
637H ALA* 1.3 74.4 - - - +
639H TYR* 1.3 57.6 + - - +
641H LEU* 3.4 24.3 - - + +
642H GLY 3.4 15.4 + - - -
657H HIS* 3.7 25.1 - - - +
660H LYS* 3.3 51.4 - - + -
661H ALA* 3.8 19.1 - - + +
664H ILE* 3.4 25.9 - - + +
496K GLU* 5.9 3.1 - - - -
499K VAL* 4.8 1.1 - - + -
500K ASP* 4.1 21.3 - - + -
503K HIS* 4.1 17.9 - + - -
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Residues in contact with TYR 639 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609H HIS* 3.8 7.9 - + - -
635H TYR* 2.8 11.3 + - + +
636H ASN* 3.5 12.8 - - - +
638H TRP* 1.3 75.1 - - - +
640H GLY* 1.3 65.3 + - - +
642H GLY 3.2 1.9 + - - -
643H MET* 3.0 49.1 + - + +
658H PHE* 3.3 39.5 - + - -
661H ALA* 4.0 2.8 - - + +
671H LEU* 3.7 25.8 - - + -
674H HIS* 3.2 38.4 + + - -
182L SER* 3.3 20.5 - - - -
183L ILE* 2.9 44.0 + - + -
184L ARG 4.8 0.7 - - - -
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Residues in contact with GLY 640 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609H HIS* 4.6 0.2 - - - -
612H VAL* 5.2 0.2 - - - +
624H PHE* 3.6 31.4 - - - -
636H ASN 3.0 12.2 + - - -
637H ALA 3.0 5.0 + - - -
639H TYR* 1.3 78.3 - - - +
641H LEU* 1.3 66.0 + - - +
643H MET* 3.1 11.5 + - - +
644H ILE* 3.0 24.6 + - - +
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Residues in contact with LEU 641 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621H LEU* 4.2 17.0 - - + +
624H PHE* 3.8 21.5 - - + -
625H ARG* 4.2 20.4 - - + -
628H ILE* 3.8 24.0 - - + -
637H ALA 2.8 14.6 + - - +
638H TRP* 3.4 39.0 - - + +
640H GLY* 1.3 70.0 - - - +
642H GLY* 1.3 58.7 + - - +
644H ILE* 3.1 10.1 + - - +
645H TYR* 2.9 36.7 + - + -
657H HIS* 4.0 13.2 - - + +
503K HIS* 4.4 17.3 - - + +
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Residues in contact with GLY 642 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638H TRP 3.4 4.8 + - - -
639H TYR 3.2 5.8 + - - -
640H GLY 3.2 1.0 - - - -
641H LEU* 1.3 75.9 - - - +
643H MET* 1.3 54.6 + - - +
645H TYR* 3.0 4.2 + - - +
646H TYR* 2.7 35.2 + - - +
654H ALA* 3.7 10.5 - - - +
657H HIS* 3.7 21.7 - - - +
658H PHE* 3.6 16.4 - - - -
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Residues in contact with MET 643 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609H HIS* 4.3 14.1 - - - +
612H VAL* 4.5 23.8 - - + -
613H LEU* 6.2 1.3 - - + -
639H TYR* 3.0 64.6 + - + +
640H GLY* 3.4 7.4 - - - +
642H GLY* 1.3 74.3 - - - +
644H ILE* 1.3 59.3 + - + +
646H TYR* 3.1 8.4 + - - +
647H LYS* 2.9 42.8 + - + +
658H PHE* 3.4 10.4 - - + -
674H HIS* 4.7 10.3 - - + +
182L SER* 4.8 8.5 - - - -
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Residues in contact with ILE 644 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612H VAL* 3.8 17.5 - - + -
617H LEU* 3.5 29.8 - - + +
620H ALA* 3.7 9.0 - - + -
621H LEU* 3.6 40.8 - - + +
624H PHE* 3.3 33.0 - - + -
640H GLY 3.0 12.9 + - - +
641H LEU 3.1 5.1 + - - +
643H MET* 1.3 76.5 - - - +
645H TYR* 1.3 60.8 + - - +
647H LYS* 3.5 6.3 + - - +
648H GLN* 3.1 34.0 + - - +
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Residues in contact with TYR 645 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621H LEU* 3.8 24.2 - - + +
625H ARG* 3.6 24.3 + - - -
641H LEU* 2.9 29.2 + - + -
642H GLY 3.7 5.4 - - - +
644H ILE* 1.3 73.0 - - - +
646H TYR* 1.3 60.1 + - - +
648H GLN* 3.4 24.3 + - - +
649H GLU 3.0 20.4 + - - -
650H LYS* 3.1 27.1 + - + +
653H LEU* 3.7 24.7 - - + -
654H ALA* 4.2 18.2 - - - +
657H HIS* 3.2 37.0 - + - -
503K HIS* 4.3 3.7 - + - -
519K LEU* 5.0 4.7 - - - +
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Residues in contact with TYR 646 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642H GLY 2.7 17.4 + - - +
643H MET* 3.4 13.2 - - - +
645H TYR* 1.3 73.0 - - - +
647H LYS* 1.3 69.2 - - + +
649H GLU* 2.9 22.7 + - - +
651H PHE* 3.6 32.0 - + - -
654H ALA* 3.8 12.3 - - + +
658H PHE* 4.7 4.5 - + + -
674H HIS* 6.4 0.7 - - - -
677H VAL* 4.8 17.4 - - + +
678H VAL* 3.7 32.1 - - + -
681H ALA* 5.0 3.3 - - + +
167L ILE 4.5 18.3 + - - -
168L GLY* 4.9 5.4 + - - -
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Residues in contact with LYS 647 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394A TYR* 3.5 23.8 - - + -
612H VAL* 3.9 33.9 + - + +
613H LEU* 5.4 3.4 - - - +
615H GLU* 5.4 5.8 - - + +
617H LEU* 4.1 27.6 - - + -
643H MET* 2.9 27.9 + - + +
644H ILE* 3.8 5.2 - - - +
646H TYR* 1.3 86.9 - - + +
648H GLN* 1.3 60.4 + - - +
649H GLU* 3.1 5.1 + - - +
163L GLU* 3.6 29.7 + - - +
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Residues in contact with GLN 648 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394A TYR* 3.3 29.4 - - + +
1395A LEU* 4.5 8.2 - - + +
617H LEU* 3.9 17.3 - - + +
618H ASP* 4.0 15.0 - - - +
621H LEU* 3.9 13.9 - - - +
644H ILE* 3.1 32.3 + - - +
645H TYR* 3.6 35.2 - - - +
646H TYR 3.3 0.2 - - - -
647H LYS* 1.3 74.1 - - - +
649H GLU* 1.3 65.3 + - - +
650H LYS* 3.3 33.5 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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