Contacts of the helix formed by residues 515 - 531 (chain C) in PDB entry 1EF1
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 ASN 515 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLU* 3.9 13.9 + - - -
193A LYS* 4.5 2.6 - - - +
511C GLU* 2.6 46.8 + - + +
512C ALA 3.1 18.0 - - - +
514C LYS* 1.3 72.1 - - - +
516C GLU* 1.3 63.4 + - - +
517C ARG* 3.1 22.0 + - - +
518C VAL* 3.1 27.4 + - + +
519C GLN* 3.2 11.4 + - - +
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Residues in contact with GLU 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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514C LYS 4.0 2.8 + - - -
515C ASN* 1.3 71.0 + - - +
517C ARG* 1.3 60.8 + - - +
519C GLN* 3.4 14.9 + - - +
520C LYS* 2.9 28.8 + - - +
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Residues in contact with ARG 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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515C ASN* 3.1 9.0 + - - +
516C GLU* 1.3 75.3 - - - +
518C VAL* 1.3 60.0 + - + +
520C LYS* 3.3 6.6 + - - +
521C HIS* 2.8 47.4 + - + +
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Residues in contact with VAL 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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124A LEU* 4.3 2.7 - - + -
128A TYR* 3.8 17.3 - - - +
190A GLU* 3.4 26.5 - - - +
194A ILE* 3.8 23.3 - - + -
511C GLU* 4.8 0.7 - - + -
512C ALA* 3.9 26.2 - - + +
515C ASN* 3.1 27.6 + - + +
517C ARG* 1.3 75.1 - - + +
519C GLN* 1.3 59.6 + - - +
521C HIS* 3.1 8.7 + - - +
522C LEU* 2.9 38.4 + - + +
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Residues in contact with GLN 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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512C ALA* 3.0 28.9 + - + +
513C GLU* 4.3 11.4 + - - +
515C ASN 3.2 11.4 + - - +
516C GLU* 3.5 14.6 - - - +
518C VAL* 1.3 80.8 - - - +
520C LYS* 1.3 62.3 + - - +
522C LEU* 3.5 6.2 + - - +
523C LYS* 3.2 32.3 + - + +
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Residues in contact with LYS 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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175A TRP* 4.3 14.1 - - - -
178A GLU* 4.7 8.1 + - - -
516C GLU 2.9 17.3 + - - +
517C ARG* 3.7 5.8 - - - +
519C GLN* 1.3 74.5 - - - +
521C HIS* 1.3 95.4 + - + +
523C LYS* 3.4 6.5 + - - +
524C ALA* 3.1 30.6 + - - +
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Residues in contact with HIS 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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124A LEU* 4.0 20.2 - - + -
128A TYR* 3.7 22.4 + - - -
175A TRP* 3.6 17.7 - + + -
178A GLU* 3.6 37.1 + - + +
179A HIS* 4.3 7.8 + + - -
517C ARG* 2.8 30.8 + - + +
518C VAL* 3.1 7.8 + - - +
520C LYS* 1.3 99.0 + - + +
522C LEU* 1.3 58.1 + - - +
524C ALA* 3.2 4.5 + - - +
525C LEU* 2.9 33.7 + - + +
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Residues in contact with LEU 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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120A GLU* 4.0 13.9 - - + +
121A THR* 3.8 39.5 - - + +
124A LEU* 3.7 23.3 - - + -
194A ILE* 6.0 3.8 - - + -
512C ALA* 4.0 26.2 - - + -
518C VAL* 2.9 23.2 + - + +
519C GLN* 3.9 5.4 - - - +
521C HIS* 1.3 76.6 - - - +
523C LYS* 1.3 58.4 + - + +
525C LEU* 3.3 5.1 + - - +
526C THR* 2.9 32.5 + - - -
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Residues in contact with LYS 523 (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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519C GLN* 3.2 27.5 + - + +
520C LYS* 3.7 7.6 - - - +
521C HIS 3.2 0.2 - - - -
522C LEU* 1.3 72.7 - - + +
524C ALA* 1.3 66.0 + - - +
526C THR* 3.3 26.6 + - - +
527C SER* 3.3 15.6 + - - -
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Residues in contact with ALA 524 (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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175A TRP* 4.0 11.0 - - + -
520C LYS* 3.1 26.5 + - - +
521C HIS 3.4 8.7 - - - +
523C LYS* 1.3 78.4 - - - +
525C LEU* 1.3 60.4 + - - +
527C SER* 3.1 8.9 + - - -
528C GLU* 2.9 43.0 + - - +
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Residues in contact with LEU 525 (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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120A GLU* 3.3 33.2 - - + +
123A VAL* 3.5 24.0 - - + -
124A LEU* 3.7 28.5 - - + +
175A TRP* 3.3 39.5 - - + +
521C HIS 2.9 19.8 + - - +
522C LEU* 3.3 6.5 + - - +
524C ALA* 1.3 73.1 - - - +
526C THR* 1.3 66.0 + - - +
528C GLU* 4.1 7.6 - - - +
529C LEU* 3.1 37.6 + - + +
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Residues in contact with THR 526 (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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120A GLU* 3.8 27.8 + - - +
522C LEU* 2.9 17.9 + - - +
523C LYS* 3.6 23.2 + - - +
524C ALA 3.2 0.6 - - - -
525C LEU* 1.3 77.1 - - - +
527C SER* 1.3 62.3 + - - +
529C LEU* 4.0 1.0 - - - +
530C ALA* 3.1 24.3 + - + +
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Residues in contact with SER 527 (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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523C LYS 3.3 10.3 + - - -
524C ALA* 3.1 10.8 + - - -
526C THR* 1.3 78.3 - - - +
528C GLU* 1.3 64.3 + - - +
529C LEU 3.2 1.0 + - - -
530C ALA* 3.2 18.9 + - - +
531C ASN* 4.3 4.3 + - - +
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Residues in contact with GLU 528 (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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171A ARG* 3.0 42.0 + - - +
174A VAL* 5.7 3.2 - - - +
175A TRP* 3.1 41.6 + - - -
524C ALA* 2.9 24.3 + - - +
525C LEU* 4.0 8.8 - - + +
526C THR 3.5 0.2 - - - -
527C SER* 1.3 77.2 - - - +
529C LEU* 1.3 61.3 + - + +
531C ASN* 4.6 5.0 + - - +
532C ALA 4.8 0.9 + - - -
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Residues in contact with LEU 529 (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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119A PRO* 4.1 28.7 - - + +
120A GLU* 4.2 12.8 - - - +
123A VAL* 4.1 12.8 - - + -
161A HIS* 3.9 23.9 - - + +
163A LEU* 4.8 2.0 - - + -
168A TRP* 4.0 27.8 - - + -
171A ARG* 3.6 22.2 - - + +
525C LEU* 3.1 28.5 + - + +
526C THR 4.4 1.1 - - - +
528C GLU* 1.3 77.9 - - + +
530C ALA* 1.3 57.0 + - - +
531C ASN 3.1 3.1 - - - -
532C ALA* 2.8 25.8 + - + +
533C ARG* 3.0 13.5 + - - +
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Residues in contact with ALA 530 (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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526C THR* 3.1 15.5 + - + +
527C SER* 3.2 15.1 + - - +
529C LEU* 1.3 75.0 - - - +
531C ASN* 1.3 61.6 - - - +
532C ALA 3.6 0.3 + - - -
533C ARG* 3.8 17.2 + - - +
535C GLU* 5.6 2.3 - - - +
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Residues in contact with ASN 531 (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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162A LYS* 6.1 0.3 - - - +
171A ARG* 5.8 2.0 - - - +
527C SER 4.3 3.4 + - - +
528C GLU 4.6 4.7 + - - +
529C LEU 3.1 0.8 - - - -
530C ALA* 1.3 80.2 - - - +
532C ALA* 1.3 59.2 + - - +
533C ARG 3.5 2.9 - - - +
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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