Contacts of the strand formed by residues 515 - 522 (chain C) in PDB entry 3EI4
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 ALA 515 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511C ALA* 3.0 10.7 - - - +
512C VAL* 2.5 42.2 + - + +
514C ARG* 1.3 75.3 - - - +
516C LEU* 1.3 59.3 + - - +
517C TYR* 3.8 28.0 - - + +
532C THR 3.6 9.2 - - - +
533C GLU* 3.8 17.6 + - - +
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Residues in contact with LEU 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C VAL* 3.9 15.3 - - + -
510C VAL 3.3 16.8 - - - +
511C ALA* 3.5 18.2 - - + -
514C ARG 3.8 0.2 + - - -
515C ALA* 1.3 73.9 - - - +
517C TYR* 1.3 62.7 + - - +
518C TYR 4.2 0.2 - - - -
530C SER 3.9 0.2 - - - +
531C HIS* 3.3 4.7 - - - +
532C THR* 3.0 38.5 + - - +
534C MET* 3.7 34.3 - - + -
538C VAL* 4.3 1.1 - - + -
541C LEU* 3.9 13.0 - - + -
558C ILE* 3.8 15.3 - - + -
569C LEU* 4.0 5.6 - - + -
574C PHE* 3.6 32.8 - - + -
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Residues in contact with TYR 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C TRP* 3.5 32.5 - + + -
492C GLU* 3.1 29.1 + - + +
493C PRO* 4.2 12.3 - - + +
508C VAL 3.7 0.2 - - - +
509C VAL* 3.4 5.7 - - - +
510C VAL* 3.1 38.7 + - + +
512C VAL* 4.0 16.3 - - + +
515C ALA* 3.8 28.3 - - + +
516C LEU* 1.3 75.5 - - - +
518C TYR* 1.3 61.1 + - - +
519C LEU* 3.7 19.7 + - + +
528C GLN* 3.9 11.9 - - + -
530C SER 3.3 5.6 - - - +
531C HIS* 4.0 21.5 - - + -
574C PHE* 4.4 2.7 - - - -
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Residues in contact with TYR 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C GLN* 3.4 38.2 + - + +
508C VAL 3.3 10.3 - - - -
509C VAL* 4.2 3.1 - - + -
517C TYR* 1.3 73.4 - - - +
519C LEU* 1.3 78.5 + - - +
520C GLN* 3.4 23.8 + - + -
528C GLN 3.9 0.3 - - - -
529C ILE* 2.9 58.8 + - + +
530C SER* 2.9 28.8 + - - +
552C LEU* 4.7 0.3 - - - +
571C LEU* 3.8 30.7 - - + +
572C PRO* 4.2 15.9 - - + -
574C PHE* 3.8 15.4 - - + -
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Residues in contact with LEU 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476C VAL* 4.4 12.8 - - + -
490C TRP* 3.4 57.9 - - + +
507C GLN* 3.7 0.2 - - - -
508C VAL* 2.9 50.9 + - + +
510C VAL* 4.9 2.0 - - + -
517C TYR* 3.7 17.7 - - + +
518C TYR* 1.3 89.2 - - - +
520C GLN* 1.3 65.8 + - - +
526C LEU* 4.4 14.6 - - + +
527C ARG 3.6 9.2 - - - +
528C GLN* 3.6 17.9 - - + -
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Residues in contact with GLN 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C SER 3.8 7.2 - - - +
507C GLN* 4.9 0.2 - - - +
518C TYR* 3.4 27.7 + - + +
519C LEU* 1.3 77.8 - - - +
521C ILE* 1.3 63.4 + - - +
522C HIS* 3.6 30.0 + - + +
525C GLU 3.1 4.9 - - - +
526C LEU* 3.6 3.6 - - - -
527C ARG* 2.8 39.5 + - - +
529C ILE* 3.4 31.8 - - + +
552C LEU* 4.1 17.0 - - - +
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Residues in contact with ILE 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C VAL* 3.3 50.7 - - + -
464C ALA* 4.0 10.5 - - + +
465C HIS* 3.2 16.2 - - - -
467C GLN* 3.6 15.0 - - - +
469C ILE* 4.4 2.9 - - + -
478C LEU* 3.9 11.4 - - + -
503C CYS* 4.3 1.8 - - - -
505C SER 3.7 3.8 - - - +
506C SER* 3.0 36.3 + - - +
507C GLN 3.8 4.9 - - - +
508C VAL* 3.9 25.6 - - + -
520C GLN* 1.3 73.3 - - - +
522C HIS* 1.3 70.2 + - - +
525C GLU 3.8 1.8 - - - -
526C LEU* 4.4 10.3 - - + -
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Residues in contact with HIS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C HIS* 3.4 14.7 - + - -
467C GLN* 3.6 9.5 + - - +
478C LEU* 3.9 1.2 - - - +
520C GLN* 3.6 40.6 + - + +
521C ILE* 1.3 80.3 + - - +
523C PRO* 1.4 78.6 - - + +
524C GLN 3.0 1.4 + - - -
525C GLU* 2.8 33.5 + - + +
527C ARG* 3.1 46.3 + - + +
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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