Contacts of the helix formed by residues 654 - 660 (chain A) in PDB entry 3L4U
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 PRO 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A TYR* 3.4 44.4 - - + +
558A LEU* 3.8 21.7 - - + +
562A LEU* 5.3 2.0 - - + -
650A THR* 4.9 2.2 - - + +
652A ALA 4.3 1.8 - - - +
653A ARG* 1.4 95.1 - - + +
655A LEU* 1.3 66.5 + - + +
656A LEU* 4.0 10.3 - - + -
657A HIS* 3.1 44.0 + - + +
668A VAL 5.4 2.9 - - - +
671A GLN 5.6 0.7 - - - +
672A PHE* 5.1 1.1 - - + -
673A LEU* 3.8 3.7 - - - +
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Residues in contact with LEU 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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654A PRO* 1.3 71.8 - - - +
656A LEU* 1.3 58.7 + - - +
658A GLU* 3.1 4.5 + - - +
659A PHE* 2.8 31.2 + - + +
665A THR* 4.2 18.6 - - + -
668A VAL* 3.9 29.8 + - + -
671A GLN* 3.9 19.2 + - - +
672A PHE* 3.7 28.7 - - - -
673A LEU* 4.0 11.9 - - + -
679A LEU* 3.8 25.4 - - + -
694A TYR* 4.4 7.6 - - + +
696A PRO* 3.8 26.7 - - + -
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Residues in contact with LEU 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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178A TYR* 3.5 50.3 - - + +
188A TYR* 4.1 7.0 - - + -
221A LEU* 5.5 0.4 - - + -
223A LEU* 4.2 15.9 - - + -
270A PRO* 4.2 7.3 - - + +
654A PRO* 3.1 16.7 - - + -
655A LEU* 1.3 76.7 - - - +
657A HIS* 1.3 81.7 + - + +
658A GLU 3.2 0.2 - - - -
659A PHE 3.7 1.8 - - - +
660A TYR* 3.1 29.2 + - - +
665A THR* 3.5 32.8 + - - +
666A TRP* 3.7 16.4 - - + +
668A VAL 5.3 2.9 - - - +
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Residues in contact with HIS 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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178A TYR* 5.9 1.2 - - - -
188A TYR* 4.3 2.4 + - - -
221A LEU* 4.3 6.4 - - + +
269A THR* 5.3 1.2 - - - -
270A PRO* 3.4 34.9 - - + +
271A GLU* 2.8 35.1 + - + +
274A VAL* 4.2 9.6 - - + -
562A LEU* 3.6 29.7 - - + +
650A THR* 4.4 1.8 - - + -
653A ARG* 3.6 22.0 - - + -
654A PRO* 3.1 33.5 + - + +
656A LEU* 1.3 89.6 - - + +
658A GLU* 1.3 64.4 + - - +
660A TYR* 3.4 17.5 - - - -
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Residues in contact with GLU 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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271A GLU* 4.8 3.8 - - - +
653A ARG* 2.7 34.3 + - - -
654A PRO 4.0 0.2 + - - -
655A LEU 3.1 3.7 + - - +
657A HIS* 1.3 85.2 - - - +
659A PHE* 1.3 82.7 + - + +
660A TYR* 3.7 7.5 + - - -
661A GLU* 3.6 12.8 - - - +
673A LEU* 3.6 21.1 - - + -
676A PRO* 3.7 15.5 - - + +
730A ARG* 2.8 40.2 + - - +
733A TYR* 4.2 3.3 + - - -
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Residues in contact with PHE 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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655A LEU* 2.8 27.2 + - - +
656A LEU 3.9 0.4 - - - -
658A GLU* 1.3 92.7 - - + +
660A TYR* 1.3 58.0 + - - +
661A GLU* 3.1 14.4 - - - +
662A ASP* 2.9 24.7 + - + +
665A THR* 3.0 28.9 + - + -
673A LEU* 4.5 9.2 - - + -
696A PRO* 3.5 31.0 - - + -
697A ASP* 4.0 15.5 - - + +
698A ALA* 4.0 11.4 - - + -
700A TRP* 3.6 27.4 - + - -
730A ARG* 3.6 40.4 - - - -
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Residues in contact with TYR 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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223A LEU* 4.0 22.9 - - + -
226A ALA* 3.5 15.0 - - - -
227A SER 3.5 18.4 - - - -
228A GLY* 3.3 19.3 - - - -
269A THR* 3.5 31.0 - - + +
270A PRO* 3.8 10.3 - - + -
656A LEU 3.1 15.2 + - - +
657A HIS 3.4 26.2 - - - -
658A GLU 4.3 6.7 - - - -
659A PHE* 1.3 74.8 - - - +
661A GLU* 1.3 88.3 + - + +
662A ASP 3.1 1.1 - - - -
665A THR* 4.5 0.7 - - - -
666A TRP* 2.9 27.3 + - - +
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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