Contacts of the helix formed by residues 650 - 662 (chain A) in PDB entry 4A8W
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A PRO* 5.0 1.1 - - - -
168A GLU* 4.7 4.4 + - - -
648A GLY 4.1 1.4 + - - -
649A VAL* 1.3 76.5 - - - +
651A VAL* 1.3 64.6 + - - +
652A GLU* 3.2 26.1 + - - +
653A LYS* 3.1 39.5 + - - +
654A THR* 3.3 12.7 + - - +
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Residues in contact with VAL 651 (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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140A PRO* 3.9 28.0 - - + +
141A VAL* 3.9 13.9 - - - -
142A PRO* 4.1 19.8 - - + +
649A VAL 3.7 1.8 + - - -
650A SER* 1.3 70.7 - - - +
652A GLU* 1.4 69.1 + - + +
654A THR* 3.6 8.5 - - - +
655A GLU* 2.7 43.3 + - + +
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Residues in contact with GLU 652 (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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650A SER* 3.1 25.2 + - - +
651A VAL* 1.4 92.6 + - + +
653A LYS* 1.3 62.0 + - + +
655A GLU* 3.8 9.4 - - - +
656A ARG* 3.4 22.9 + - - +
659A ARG* 5.5 0.5 + - - -
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Residues in contact with LYS 653 (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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168A GLU* 3.6 43.2 + - + +
171A LEU* 4.2 9.2 - - + +
172A GLU* 4.7 13.1 + - + +
649A VAL* 4.2 11.4 - - + -
650A SER* 3.1 23.4 + - - +
652A GLU* 1.3 77.1 - - + +
654A THR* 1.3 62.2 + - - +
656A ARG* 3.7 7.4 + - - +
657A PHE* 3.2 22.0 + - - +
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Residues in contact with THR 654 (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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140A PRO* 4.5 1.5 - - - +
141A VAL 2.7 27.1 + - - +
143A LEU* 3.7 32.5 - - + +
171A LEU* 3.9 24.0 - - + -
285A ALA* 5.1 11.2 - - + -
649A VAL* 4.1 3.8 - - + -
650A SER 3.3 14.4 + - - +
651A VAL* 3.4 9.4 + - - +
653A LYS* 1.3 73.3 - - - +
655A GLU* 1.3 58.1 + - - +
657A PHE* 3.2 2.9 + - - +
658A LEU* 2.8 37.8 + - - +
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Residues in contact with GLU 655 (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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140A PRO* 3.7 31.8 - - + +
651A VAL* 2.7 29.9 + - + +
652A GLU* 3.8 10.7 - - - +
654A THR* 1.3 73.4 + - - +
656A ARG* 1.3 55.4 + - - +
658A LEU* 3.5 1.6 + - - +
659A ARG* 3.1 57.4 + - - +
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Residues in contact with ARG 656 (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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172A GLU* 4.8 16.2 - - - +
652A GLU 3.4 14.8 + - - +
653A LYS* 3.9 7.9 - - - +
654A THR 3.3 0.4 - - - -
655A GLU* 1.3 75.0 - - - +
657A PHE* 1.3 66.9 + - - +
659A ARG* 3.6 23.9 + - - +
660A SER* 3.5 18.2 + - - -
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Residues in contact with PHE 657 (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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171A LEU* 3.3 37.2 - - + +
174A ALA* 3.8 24.7 - - + -
282A PRO* 3.4 40.8 - - + -
285A ALA* 3.6 24.2 - - + -
286A VAL* 4.5 4.5 - - + -
352A TRP* 3.8 13.9 - + - -
353A TRP* 3.8 6.7 - + - -
653A LYS 3.2 12.0 + - - +
654A THR 3.2 8.6 + - - +
656A ARG* 1.3 79.3 - - - +
658A LEU* 1.3 67.0 + - + +
660A SER* 2.6 25.9 + - - -
661A VAL* 3.4 25.9 + - + +
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Residues in contact with LEU 658 (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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138A LEU* 4.6 0.9 - - + +
139A GLU 4.2 3.6 - - - -
140A PRO* 3.7 39.9 - - + -
285A ALA* 3.3 25.6 - - + +
286A VAL* 3.8 25.6 - - + -
289A PRO* 4.3 9.2 - - + -
654A THR* 2.8 20.5 + - - +
655A GLU 3.9 3.8 - - - +
657A PHE* 1.3 78.3 - - + +
659A ARG* 1.3 62.0 + - - +
661A VAL* 3.2 3.1 + - + +
662A MET* 3.1 62.0 + - + +
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Residues in contact with ARG 659 (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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652A GLU 5.5 0.6 + - - -
655A GLU* 3.1 56.1 + - - +
656A ARG* 3.7 28.6 - - - +
657A PHE 3.3 0.2 - - - -
658A LEU* 1.3 74.8 - - - +
660A SER* 1.3 60.9 + - - +
661A VAL 3.6 0.3 + - - -
662A MET* 3.7 15.7 - - - +
664A ARG 5.5 3.9 - - - +
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Residues in contact with SER 660 (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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175A GLU* 4.6 9.4 + - - -
350A ALA* 3.6 14.0 - - - +
352A TRP* 3.5 25.5 + - - -
656A ARG 3.5 7.3 + - - -
657A PHE* 2.6 25.1 + - - -
659A ARG* 1.3 79.8 - - - +
661A VAL* 1.4 57.3 + - - +
662A MET 4.8 1.0 - - - +
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Residues in contact with VAL 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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286A VAL* 4.0 9.6 - - + -
349A TYR* 3.4 26.3 - - + -
350A ALA* 2.8 34.0 + - - -
352A TRP* 3.6 22.7 - - + -
353A TRP* 3.6 26.5 - - + -
657A PHE* 3.4 37.7 - - + +
658A LEU* 3.2 8.0 + - - +
660A SER* 1.4 76.7 - - - +
662A MET* 1.3 67.5 + - + +
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Residues in contact with MET 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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136A SER 4.3 9.0 - - - +
137A ASP* 5.6 0.2 - - - -
138A LEU* 3.3 51.1 - - + +
140A PRO* 5.9 0.2 - - + -
286A VAL* 6.0 0.2 - - - -
348A GLY 4.4 1.4 - - - +
349A TYR* 3.7 25.1 - - + +
658A LEU* 3.1 40.2 + - + +
659A ARG* 3.7 13.8 - - - +
660A SER 4.8 1.0 - - - +
661A VAL* 1.3 87.9 - - + +
663A PRO* 1.4 75.2 - - + +
664A ARG* 3.6 2.8 + - - +
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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