Contacts of the helix formed by residues 515 - 531 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B GLU* 3.7 12.5 + - - -
193B LYS* 4.4 2.4 - - - +
511D GLU* 2.6 44.4 + - - +
512D ALA 3.4 8.1 - - - +
513D GLU 3.5 0.8 - - - -
514D LYS* 1.3 73.6 - - - +
516D GLU* 1.3 63.6 + - - +
517D ARG* 3.2 21.3 + - - +
518D VAL* 3.1 26.3 + - + +
519D GLN* 3.0 18.9 + - - -
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Residues in contact with GLU 516 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D GLU 5.5 0.2 + - - -
514D LYS 4.0 2.8 + - - -
515D ASN* 1.3 73.0 + - - +
517D ARG* 1.3 57.0 + - - +
519D GLN* 3.4 13.9 + - - +
520D LYS* 2.9 29.3 + - - +
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Residues in contact with ARG 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515D ASN* 3.2 11.4 + - - +
516D GLU* 1.3 74.4 - - - +
518D VAL* 1.3 62.8 + - + +
520D LYS* 3.4 5.9 + - - +
521D HIS* 2.9 49.0 + - + +
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Residues in contact with VAL 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.1 3.1 - - + -
128B TYR* 4.0 15.3 - - - +
190B GLU* 3.3 26.2 - - - +
194B ILE* 3.8 23.8 - - + -
511D GLU* 4.6 0.9 - - + -
512D ALA* 4.3 12.3 - - + +
515D ASN* 3.1 28.1 + - + +
517D ARG* 1.3 76.7 - - + +
519D GLN* 1.3 58.1 + - - +
521D HIS* 3.3 7.2 + - - +
522D LEU* 2.9 47.0 + - + +
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Residues in contact with GLN 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512D ALA* 2.8 33.4 + - + +
513D GLU* 4.2 12.9 + - - +
515D ASN 3.0 6.7 + - - +
516D GLU* 3.5 15.3 - - - +
518D VAL* 1.3 75.4 - - - +
520D LYS* 1.3 64.9 + - - +
522D LEU* 3.5 5.1 + - - +
523D LYS* 3.1 37.9 + - + +
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Residues in contact with LYS 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B TRP* 3.7 16.6 - - - -
178B GLU* 4.7 8.9 + - - -
516D GLU 2.9 17.8 + - - +
517D ARG* 3.8 5.6 - - - +
519D GLN* 1.3 75.4 - - - +
521D HIS* 1.3 94.0 + - + +
523D LYS* 3.2 9.3 + - - +
524D ALA* 3.0 31.3 + - - +
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Residues in contact with HIS 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.0 20.6 - - + -
128B TYR* 3.7 23.4 + - - -
175B TRP* 3.4 23.2 - + + -
178B GLU* 4.0 23.2 - - + +
179B HIS* 4.6 6.5 + + - -
517D ARG* 2.9 35.0 + - + +
518D VAL* 3.4 5.8 - - - +
520D LYS* 1.3 105.6 + - + +
522D LEU* 1.3 57.6 + - - +
524D ALA* 3.3 4.2 + - - +
525D LEU* 2.9 32.9 + - - +
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Residues in contact with LEU 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU* 3.9 13.3 - - + +
121B THR* 3.6 41.1 - - + +
124B LEU* 3.7 21.1 - - + -
194B ILE* 5.6 5.2 - - + -
512D ALA* 4.1 18.4 - - + -
518D VAL* 2.9 34.2 + - + +
519D GLN* 4.0 4.9 - - - +
520D LYS 3.4 0.2 - - - -
521D HIS* 1.3 75.6 - - - +
523D LYS* 1.3 58.3 + - + +
525D LEU* 3.4 4.9 + - + +
526D THR* 2.9 33.5 + - - -
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Residues in contact with LYS 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519D GLN* 3.1 32.6 + - + +
520D LYS* 3.2 12.5 + - - +
522D LEU* 1.3 71.5 - - + +
524D ALA* 1.3 66.3 + - - +
526D THR* 3.2 18.3 + - - -
527D SER* 3.4 15.1 + - - -
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Residues in contact with ALA 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TRP* 3.9 19.3 - - + -
520D LYS* 3.0 22.6 + - - +
521D HIS 3.5 8.5 - - - +
523D LYS* 1.3 76.5 - - - +
525D LEU* 1.3 61.7 + - - +
527D SER* 3.1 10.8 + - - -
528D GLU* 3.0 32.6 + - - +
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Residues in contact with LEU 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU* 3.4 33.9 - - + +
123B VAL* 4.0 16.8 - - + -
124B LEU* 3.7 31.2 - - + +
175B TRP* 3.3 39.5 - - + +
521D HIS 2.9 19.9 + - - +
522D LEU* 3.7 5.8 - - - +
524D ALA* 1.3 76.2 - - - +
526D THR* 1.3 64.1 + - - +
528D GLU* 3.6 9.0 - - - +
529D LEU* 3.1 38.4 + - + +
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Residues in contact with THR 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU* 3.9 30.2 + - - +
522D LEU 2.9 19.5 + - - -
523D LYS* 3.5 12.7 + - - -
524D ALA 3.2 0.4 - - - -
525D LEU* 1.3 77.8 - - - +
527D SER* 1.3 59.9 + - - +
529D LEU* 3.9 1.7 - - - +
530D ALA* 3.1 22.6 + - + +
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Residues in contact with SER 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D LYS 3.4 9.4 + - - -
524D ALA* 3.1 11.8 + - - -
526D THR* 1.3 75.9 - - - +
528D GLU* 1.3 67.1 + - - +
530D ALA* 3.1 20.9 + - - +
531D ASN* 4.4 2.8 + - - +
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Residues in contact with GLU 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ARG* 2.9 40.4 + - - +
174B VAL* 6.0 1.8 - - - +
175B TRP* 2.9 43.3 + - - -
524D ALA* 3.0 20.6 + - - +
525D LEU* 3.6 9.5 - - - +
527D SER* 1.3 81.7 - - - +
529D LEU* 1.3 60.9 + - + +
531D ASN* 4.7 5.2 + - - +
532D ALA 4.8 0.9 + - - -
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Residues in contact with LEU 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B PRO* 4.1 10.1 - - + +
120B GLU* 4.1 31.9 - - + +
123B VAL* 4.1 13.7 - - + -
161B HIS* 3.9 21.7 - - + +
163B LEU* 4.7 4.3 - - + -
168B TRP* 4.0 28.9 - - + -
171B ARG* 4.0 18.2 - - + +
525D LEU* 3.1 29.2 + - + +
526D THR* 3.9 2.2 - - - +
528D GLU* 1.3 75.5 - - + +
530D ALA* 1.3 64.8 + - - +
531D ASN 3.2 2.7 - - - -
532D ALA* 3.2 5.5 + - + +
533D ARG* 3.1 25.2 + - - +
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Residues in contact with ALA 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D THR* 3.1 14.1 + - + +
527D SER* 3.1 17.5 + - - +
529D LEU* 1.3 77.3 - - - +
531D ASN* 1.3 61.5 + - - +
533D ARG* 3.8 15.4 + - - +
535D GLU* 5.3 2.4 - - - +
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Residues in contact with ASN 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LYS* 5.7 1.9 - - - +
171B ARG* 5.8 2.7 - - - +
527D SER 4.4 2.8 + - - +
528D GLU 5.1 4.9 - - - +
529D LEU 3.2 0.6 - - - -
530D ALA* 1.3 80.5 - - - +
532D ALA* 1.3 62.3 + - - +
533D ARG 3.3 4.3 + - - +
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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