Contacts of the helix formed by residues 629 - 644 (chain K) in PDB entry 5ANC
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 GLU 629 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624K PRO* 4.0 5.6 - - - +
625K LYS 4.1 9.4 - - - +
626K HIS* 3.3 19.6 + - + +
627K PRO 3.2 1.8 - - - -
628K SER* 1.3 102.3 - - - +
630K MET* 1.3 61.0 + - - +
631K PRO 3.6 1.3 - - - -
632K GLN* 3.1 36.1 - - - +
681K ILE* 3.8 38.3 - - + +
682K HIS* 6.6 0.4 - - + -
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Residues in contact with MET 630 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J VAL* 4.4 22.2 - - + +
121J ASN 4.8 2.0 - - - +
122J PRO* 3.9 29.6 - - + -
123J GLU* 4.3 7.9 - - - +
132J LEU* 3.7 31.6 - - + -
135J ARG* 4.0 23.1 - - - +
166J LYS* 5.0 12.3 - - - +
624K PRO* 3.9 18.3 - - + +
626K HIS 4.5 3.1 - - - +
627K PRO* 3.5 19.3 - - + +
628K SER 3.4 0.2 - - - -
629K GLU* 1.3 78.1 - - - +
631K PRO* 1.4 70.3 - - + +
632K GLN 3.2 0.9 + - - -
633K LEU* 3.6 15.6 + - - +
634K VAL 4.1 0.5 + - - -
657K HIS* 4.0 15.2 + - - -
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Residues in contact with PRO 631 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J GLU* 3.8 37.2 - - + +
166J LYS* 5.3 3.8 - - - +
627K PRO 4.7 1.1 - - - +
628K SER* 3.6 15.5 - - - +
630K MET* 1.4 91.3 - - + +
632K GLN* 1.3 59.8 + - + +
633K LEU 3.2 0.7 - - - -
634K VAL* 3.2 10.9 + - + +
635K LYS* 2.9 40.2 + - + +
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Residues in contact with GLN 632 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628K SER 4.5 3.2 - - - +
629K GLU* 3.1 43.8 - - - +
630K MET 3.2 0.4 - - - -
631K PRO* 1.3 78.9 - - + +
633K LEU* 1.3 57.1 + - - +
635K LYS* 3.2 36.1 + - - +
636K GLY* 2.9 26.7 + - - -
679K ALA* 3.8 18.3 - - + +
681K ILE* 3.6 18.3 - - + +
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Residues in contact with LEU 633 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622K VAL* 4.8 14.4 - - + -
624K PRO* 4.1 20.4 - - + -
630K MET 3.6 10.4 + - - +
631K PRO 3.2 0.2 - - - -
632K GLN* 1.3 77.7 - - - +
634K VAL* 1.3 57.8 + - - +
636K GLY* 3.2 3.1 + - - +
637K MET* 2.9 35.8 + - + +
656K GLU 5.7 0.4 - - - +
657K HIS* 3.9 37.0 - - + +
674K LEU* 3.7 28.4 - - + +
679K ALA* 5.3 1.8 - - - -
681K ILE* 3.9 17.6 - - + +
683K ILE* 4.4 22.7 - - + -
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Residues in contact with VAL 634 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J GLU* 5.3 6.1 - - + -
126J ARG* 4.7 3.4 - - - +
630K MET 4.3 4.3 - - - +
631K PRO* 3.2 15.1 + - + +
633K LEU* 1.3 78.5 - - - +
635K LYS* 1.3 65.4 + - + +
637K MET* 3.2 17.3 + - - +
638K LYS* 3.2 25.1 + - - +
649K ILE* 3.5 14.6 - - + +
656K GLU* 3.3 32.1 - - + +
657K HIS* 3.5 33.4 - - + +
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Residues in contact with LYS 635 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631K PRO* 2.9 24.9 + - + +
632K GLN* 3.4 38.0 + - - +
634K VAL* 1.3 77.6 - - + +
636K GLY* 1.3 62.9 - - - +
638K LYS* 3.0 39.3 + - + +
639K LEU* 3.5 8.7 + - - +
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Residues in contact with GLY 636 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632K GLN 2.9 13.5 + - - -
633K LEU 3.2 4.0 + - - -
635K LYS* 1.3 75.7 - - - +
637K MET* 1.3 50.8 + - - +
639K LEU* 2.8 33.6 + - - +
640K LEU 2.8 14.7 + - - -
674K LEU* 3.5 22.1 - - - +
679K ALA* 4.3 16.5 - - - +
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Residues in contact with MET 637 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622K VAL* 6.4 2.0 - - + -
633K LEU* 2.9 20.1 + - + +
634K VAL* 3.2 11.2 + - - +
636K GLY* 1.3 75.7 - - - +
638K LYS* 1.3 54.5 + - - +
640K LEU* 3.7 8.7 - - + -
641K ASN* 3.1 25.3 + - - +
647K VAL* 3.9 18.5 - - + +
648K GLN 3.3 25.8 - - - +
649K ILE* 3.9 15.1 - - + +
656K GLU 3.3 26.2 - - - +
657K HIS* 4.9 2.7 - - - -
658K VAL 3.7 20.2 - - - +
659K LEU* 4.0 22.9 - - + -
674K LEU* 3.9 12.6 - - + +
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Residues in contact with LYS 638 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593K LEU* 4.8 6.2 - - + +
634K VAL* 3.2 22.9 + - - +
635K LYS* 3.0 36.6 + - + +
637K MET* 1.3 75.9 - - - +
639K LEU* 1.3 62.9 + - + +
641K ASN* 3.4 17.8 - - - +
642K GLN* 3.6 12.0 + - - +
649K ILE* 4.2 17.1 - - + +
656K GLU* 5.6 2.0 + - - -
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Residues in contact with LEU 639 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417K MET* 4.1 6.8 - - + +
420K VAL* 4.9 13.9 - - + -
590K ASP* 5.1 3.8 - - - +
635K LYS 4.1 7.6 - - - +
636K GLY* 2.8 18.5 + - - +
638K LYS* 1.3 72.3 - - + +
640K LEU* 1.3 63.2 + - - +
641K ASN 3.2 0.4 - - - -
642K GLN* 3.1 37.2 + - - +
643K ALA* 3.2 12.1 + - - +
678K PHE* 3.6 47.7 - - + +
679K ALA 4.9 0.4 - - - +
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Residues in contact with LEU 640 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636K GLY 2.8 10.8 + - - +
637K MET* 3.6 13.5 - - + +
639K LEU* 1.3 74.9 - - - +
641K ASN* 1.3 59.0 + - - +
643K ALA* 3.2 4.0 + - + +
644K ASP* 2.9 55.2 + - - +
647K VAL* 3.5 27.8 - - + -
659K LEU* 3.9 15.0 - - + -
670K CYS* 4.4 9.2 - - + +
673K ASP* 4.1 11.7 - - + +
674K LEU* 3.7 29.6 - - + -
677K ARG* 5.2 0.2 - - - +
678K PHE* 3.9 23.5 - - + -
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Residues in contact with ASN 641 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414K VAL* 4.7 0.2 - - - +
592K VAL 4.6 1.1 - - - +
593K LEU* 3.6 21.6 - - + +
594K LYS* 3.8 31.3 + - - +
610K LEU* 4.6 7.1 - - - +
637K MET 3.1 13.4 + - - +
638K LYS* 3.4 12.8 - - - +
640K LEU* 1.3 76.3 - - - +
642K GLN* 1.3 61.0 + - - +
644K ASP 2.8 17.9 - - - +
645K PRO* 3.8 18.2 + - - +
647K VAL* 3.5 22.5 + - + +
649K ILE* 4.0 17.1 - - + +
650K LEU* 5.7 3.4 - - - +
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Residues in contact with GLN 642 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414K VAL* 3.6 9.5 - - - +
416K LYS* 5.1 0.3 - - - -
417K MET* 3.2 24.1 + - - +
590K ASP* 3.0 41.7 + - - +
591K PHE* 3.9 24.4 - - - +
592K VAL* 3.1 42.0 - - + +
593K LEU* 4.8 12.5 - - + +
638K LYS 3.6 14.2 + - - +
639K LEU* 3.1 22.3 + - - +
641K ASN* 1.3 78.9 - - - +
643K ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 643 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K THR* 4.2 5.9 - - - +
414K VAL* 4.4 2.4 - - - +
416K LYS* 3.3 25.0 + - - +
417K MET* 4.0 19.6 - - + +
639K LEU 3.2 1.7 + - - +
640K LEU* 3.2 8.6 + - - +
642K GLN* 1.3 82.7 - - - +
644K ASP* 1.3 68.0 + - - +
677K ARG* 3.6 28.0 - - - +
678K PHE* 3.7 17.3 - - + -
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Residues in contact with ASP 644 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K GLU* 5.0 1.4 - - + +
105K THR* 5.3 0.2 - - - -
414K VAL* 5.5 0.4 - - - -
416K LYS* 3.6 14.2 - - - +
640K LEU* 2.9 33.6 + - + +
641K ASN* 2.8 19.5 - - - +
642K GLN 5.2 0.2 - - - -
643K ALA* 1.3 86.1 - - - +
645K PRO* 1.3 76.2 - - + +
646K CYS 3.3 11.8 + - - +
647K VAL* 4.5 0.4 - - + +
666K HIS* 4.3 14.6 - - + +
669K ARG* 3.1 31.3 + - - -
670K CYS* 3.6 10.9 - - - -
673K ASP* 4.2 0.3 - - - +
677K ARG* 4.2 0.7 + - - -
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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
------------------------------------------------------------
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