Contacts of the helix formed by residues 660 - 675 (chain A) in PDB entry 5VLR
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 VAL 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A LYS* 3.6 43.1 - - + -
654A GLU* 3.3 36.1 - - + +
657A VAL* 3.6 15.7 - - + +
659A SER* 1.4 83.3 - - - +
661A ALA* 1.3 66.9 + - - +
662A LEU 3.1 3.8 + - - -
663A ARG* 3.2 8.7 + - + +
664A PHE* 2.9 46.0 + - + +
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Residues in contact with ALA 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LYS* 4.3 20.0 - - + +
463A PRO* 6.2 1.1 - - + -
654A GLU 4.7 1.8 - - - -
655A MET* 3.3 42.4 - - + +
656A HIS 5.4 0.4 - - - -
657A VAL 3.0 16.8 + - - +
658A PRO* 3.8 10.8 + - + +
660A VAL* 1.3 74.2 - - - +
662A LEU* 1.3 56.2 + - - +
665A GLY* 2.9 23.4 + - - -
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Residues in contact with LEU 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LYS* 4.8 6.9 - - - +
128A PHE* 3.6 33.7 - - + -
131A LEU* 3.7 28.9 - - + -
133A ASP* 5.6 0.2 - - - +
136A VAL* 4.3 13.9 - - + -
460A ARG* 4.5 26.0 - - + +
625A LEU* 4.5 7.6 - - + -
658A PRO 4.9 1.8 + - - -
659A SER 5.5 0.2 + - - -
660A VAL 3.3 0.8 - - - -
661A ALA* 1.3 73.6 - - - +
663A ARG* 1.4 66.7 + - - +
665A GLY* 3.0 3.5 + - - -
666A LEU* 2.9 40.1 + - + +
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Residues in contact with ARG 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 5.3 0.8 - - + -
460A ARG* 5.1 11.2 - - + +
619A LEU* 3.2 33.0 + - - -
620A LYS* 5.3 1.9 - - - +
622A GLU* 3.3 34.2 + - - +
623A SER 4.1 2.0 + - - -
624A TYR* 2.8 37.5 + - - +
625A LEU* 3.3 42.1 + - + +
627A CYS* 4.2 1.4 - - - -
630A THR* 4.0 10.1 + - - -
659A SER 5.6 2.0 - - - +
660A VAL* 3.2 12.2 + - - +
662A LEU* 1.4 79.2 - - - +
664A PHE* 1.3 73.9 + - + +
666A LEU* 3.2 12.0 + - - +
667A ILE* 3.2 22.7 + - + +
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Residues in contact with PHE 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A VAL* 4.0 20.6 - - + -
619A LEU* 4.0 22.9 - - + -
620A LYS* 4.5 9.6 - - + -
650A HIS 4.6 0.4 - - - -
651A LEU* 3.5 51.4 - - + +
654A GLU* 4.0 24.9 - - + -
655A MET* 4.0 14.4 - - - -
660A VAL* 2.9 49.8 + - + +
663A ARG* 1.3 85.4 - - + +
665A GLY* 1.3 56.7 + - - +
667A ILE* 3.2 8.1 + - + +
668A LEU* 3.0 31.4 + - - +
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Residues in contact with GLY 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.1 6.4 - - - +
128A PHE* 3.6 17.4 - - - -
655A MET* 3.7 17.0 - - - -
661A ALA 2.9 20.4 + - - -
662A LEU 3.0 1.3 + - - -
664A PHE* 1.3 73.4 - - - +
666A LEU* 1.3 63.0 + - - +
668A LEU* 3.4 5.2 + - - +
669A GLU* 3.1 23.7 + - - +
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Residues in contact with LEU 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 3.7 37.2 - - + -
136A VAL* 3.8 9.4 - - + -
139A PHE* 3.3 33.1 - - + -
140A ARG* 3.7 25.1 - - + +
144A CYS* 5.8 0.3 - - - -
625A LEU* 3.6 37.0 - - + -
662A LEU* 2.9 32.7 + - + +
663A ARG* 3.2 5.6 + - - +
665A GLY* 1.3 75.9 - - - +
667A ILE* 1.4 60.3 + - - +
669A GLU* 3.7 6.1 + - - +
670A ALA* 3.5 15.9 + - - +
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Residues in contact with ILE 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 4.1 8.3 - - + -
619A LEU* 3.8 30.5 - - + -
630A THR* 3.6 33.4 - - + +
633A LEU* 6.0 2.7 - - + -
634A LEU* 3.9 23.5 - - + +
647A LEU* 4.9 6.7 - - + -
651A LEU* 3.6 25.4 - - + -
663A ARG* 3.2 24.6 + - + +
664A PHE* 3.2 7.2 + - - +
666A LEU* 1.4 73.6 - - - +
668A LEU* 1.3 60.4 + - - +
669A GLU 3.3 0.5 + - - -
670A ALA* 3.3 5.2 + - - +
671A TYR* 2.8 28.4 + - + +
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Residues in contact with LEU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.6 25.8 - - + -
648A PHE* 3.5 52.0 - - + +
651A LEU* 3.9 15.9 - - + -
652A ARG* 4.1 12.6 - - - +
655A MET* 3.8 32.3 - - + -
664A PHE 3.0 18.7 + - - +
665A GLY* 3.8 2.9 - - - +
667A ILE* 1.3 77.0 - - - +
669A GLU* 1.4 56.5 + - - +
671A TYR* 3.8 5.7 - - + +
672A CYS* 3.0 35.9 + - - -
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Residues in contact with GLU 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE* 4.0 24.0 - - + -
121A ILE* 4.7 0.8 - - + +
125A LEU* 3.5 25.4 - - + +
128A PHE* 3.9 5.0 - - - -
140A ARG* 2.9 37.4 + - - +
144A CYS* 3.4 14.4 - - - -
665A GLY 3.1 16.1 + - - +
666A LEU* 4.0 5.5 - - - +
667A ILE 3.3 0.4 - - - -
668A LEU* 1.4 71.9 - - - +
670A ALA* 1.4 55.5 + - - +
672A CYS* 3.1 4.7 + - - +
673A ARG* 2.8 72.6 + - - +
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Residues in contact with ALA 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 4.8 0.4 - - + -
143A MET* 3.9 24.5 - - + +
144A CYS* 4.3 13.2 - - - +
147A CYS* 3.3 29.0 - - - +
634A LEU* 4.1 9.4 - - + -
666A LEU 3.5 11.2 + - - +
667A ILE* 3.3 8.0 + - - +
669A GLU* 1.4 76.8 - - - +
671A TYR* 1.4 63.8 + - - +
673A ARG* 3.2 12.1 + - - +
674A GLY 3.2 8.8 + - - -
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Residues in contact with TYR 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A CYS* 4.7 2.0 - - - -
634A LEU* 3.8 16.5 - - + +
637A ALA* 4.2 19.3 - - + -
638A LEU* 4.2 4.6 - - + +
641A ARG* 5.0 1.0 + - - +
644A GLY* 3.7 32.8 - - - -
647A LEU* 5.1 6.1 - - + -
648A PHE* 3.9 22.7 - + + -
651A LEU* 6.1 0.7 - - + -
667A ILE* 2.8 20.9 + - + +
668A LEU* 3.8 7.4 - - + +
670A ALA* 1.4 71.4 - - - +
672A CYS* 1.3 66.9 + - - +
674A GLY* 3.2 3.6 + - - -
675A SER* 3.0 51.3 + - - -
678A HIS* 3.0 37.8 - - + +
679A MET 5.7 0.7 - - - -
682A LEU* 3.6 20.8 - - + +
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Residues in contact with CYS 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE* 3.7 21.5 - - + -
120A LEU* 3.8 29.2 - - - -
121A ILE* 4.6 6.3 - - - -
648A PHE* 4.3 8.7 - - - -
668A LEU 3.0 27.1 + - - +
669A GLU 3.3 4.9 - - - +
671A TYR* 1.3 89.6 - - - +
673A ARG* 1.4 57.7 + - - +
675A SER* 2.9 17.7 + - - +
676A THR* 3.2 15.9 + - - +
679A MET* 3.8 17.3 - - + +
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Residues in contact with ARG 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS* 4.8 5.8 - - - +
113A ILE* 3.7 15.9 - - - +
114A ASN* 2.9 44.4 + - - +
117A ILE* 3.7 17.4 - - + +
125A LEU* 3.5 9.7 - - - +
140A ARG* 4.6 1.8 - - - +
144A CYS* 3.4 21.7 - - - +
147A CYS* 4.7 0.2 - - - -
148A GLU* 3.5 46.4 + - + +
151A ALA* 4.6 3.1 - - - +
669A GLU* 2.8 51.7 + - - +
670A ALA* 3.2 9.8 + - - +
672A CYS* 1.4 70.9 - - - +
674A GLY* 1.3 56.3 + - - +
675A SER 3.5 0.2 - - - -
676A THR* 4.3 14.0 - - - +
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Residues in contact with GLY 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A CYS* 3.7 23.8 - - - +
151A ALA* 3.4 9.6 - - - +
154A ARG* 2.8 38.8 + - - -
638A LEU* 3.7 9.6 - - - -
670A ALA 3.2 5.3 + - - -
671A TYR 3.2 6.5 + - - -
672A CYS 3.1 0.4 - - - -
673A ARG* 1.3 75.3 - - - +
675A SER* 1.3 55.9 + - - +
676A THR* 3.8 1.8 - - - -
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Residues in contact with SER 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 4.0 9.9 + - - +
165A TYR* 4.2 8.7 + - - -
637A ALA 4.7 2.6 + - - -
638A LEU* 3.7 7.8 - - - +
671A TYR* 3.0 50.2 + - - -
672A CYS 2.9 7.5 + - - -
674A GLY* 1.3 81.1 + - - +
676A THR* 1.3 52.7 + - - +
677A HIS* 3.2 3.1 - - - -
678A HIS* 3.0 11.2 + - - +
679A MET* 2.9 30.8 + - - +
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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