Contacts of the helix formed by residues 554 - 563 (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 ASP 554 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B GLU* 5.3 6.1 - - - -
508D ARG 4.8 2.6 - - - +
509D THR* 5.6 0.8 - - - -
510D THR* 4.2 21.5 - - + -
513D GLU* 4.8 9.3 - - - +
552D GLY 4.5 4.2 - - - +
553D ARG* 1.3 76.5 - - - +
555D LYS* 1.3 67.0 + - - +
556D TYR* 3.2 14.6 + - - +
557D LYS* 3.0 38.1 + - - +
558D THR* 3.0 25.2 + - - -
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Residues in contact with LYS 555 (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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196B GLN 3.0 24.4 + - - +
197B ASP 3.8 19.4 + - - +
198B LEU 3.0 22.8 + - - +
199B GLU* 3.8 33.0 + - + +
201B TYR* 3.4 22.2 + - - -
203B VAL* 5.3 0.2 - - - -
221B ASP* 5.2 8.5 - - - -
223B LEU* 5.9 6.7 - - + +
510D THR* 5.4 0.6 - - + +
554D ASP* 1.3 74.5 - - - +
556D TYR* 1.3 82.0 + - + +
558D THR* 3.8 4.8 - - - +
559D LEU* 3.1 32.0 + - + +
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Residues in contact with TYR 556 (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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196B GLN 3.5 14.7 + - - -
197B ASP* 2.7 30.1 + - - -
223B LEU* 5.0 5.2 - - + -
505D GLU* 3.5 23.1 - - + +
506D GLU* 3.9 8.2 - - - +
508D ARG* 3.2 73.0 + - + +
509D THR 3.7 18.2 - - - -
510D THR* 4.0 9.2 - - + -
554D ASP* 3.2 9.9 + - - +
555D LYS* 1.3 96.0 - - + +
557D LYS* 1.3 65.6 + - - +
559D LEU* 3.3 14.1 + - + +
560D ARG* 3.0 22.7 + - - +
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Residues in contact with LYS 557 (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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506D GLU 5.1 1.8 - - - -
552D GLY 4.7 14.2 + - - +
553D ARG* 5.4 2.2 - - - -
554D ASP* 3.0 31.9 + - - +
556D TYR* 1.3 74.3 - - - +
558D THR* 1.3 57.7 + - - +
560D ARG* 3.3 18.5 - - - +
561D GLN* 3.0 28.8 + - + +
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Residues in contact with THR 558 (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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235B THR* 4.1 10.4 + - + +
236B PRO* 3.9 43.3 - - + +
553D ARG* 4.0 24.9 - - - +
554D ASP 3.0 20.1 + - - -
555D LYS* 3.8 4.7 - - - -
557D LYS* 1.3 75.1 - - - +
559D LEU* 1.3 56.5 + - - +
561D GLN* 3.2 7.5 + - + +
562D ILE* 2.8 37.2 + - + +
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Residues in contact with LEU 559 (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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221B ASP* 6.0 1.1 - - - +
223B LEU* 3.7 31.2 - - + -
226B ASN* 3.7 27.8 - - - +
236B PRO* 5.2 3.4 - - + -
505D GLU* 4.1 15.7 - - + +
506D GLU* 4.6 3.4 - - + -
555D LYS* 3.1 19.3 + - + +
556D TYR* 3.4 16.6 - - + +
558D THR* 1.3 76.3 - - - +
560D ARG* 1.3 60.6 + - - +
562D ILE* 3.4 14.2 - - + +
563D ARG* 2.9 58.7 + - - +
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Residues in contact with ARG 560 (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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506D GLU* 3.8 44.9 + - + +
507D GLU* 3.8 21.2 + - - -
556D TYR 3.0 12.6 + - - +
557D LYS* 3.3 23.1 - - - +
559D LEU* 1.3 77.9 - - - +
561D GLN* 1.3 61.9 + - - +
563D ARG* 3.5 9.2 + - - +
564D GLN* 3.3 42.2 + - - +
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Residues in contact with GLN 561 (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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553D ARG* 6.1 0.6 - - - +
557D LYS* 3.0 15.7 + - + +
558D THR* 3.6 8.5 - - + +
560D ARG* 1.3 81.6 - - - +
562D ILE* 1.3 69.4 + - + +
564D GLN* 3.3 43.7 + - - +
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Residues in contact with ILE 562 (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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226B ASN* 4.4 1.6 - - - +
236B PRO* 3.3 50.5 - - + +
237B LYS* 3.2 26.2 - - - +
238B ILE* 3.7 15.6 - - - +
239B GLY* 3.0 23.1 + - - +
558D THR* 2.8 31.2 + - + +
559D LEU* 3.4 24.2 - - + +
561D GLN* 1.3 79.8 - - + +
563D ARG* 1.3 56.1 + - + +
564D GLN 3.3 2.9 - - - -
570D ARG* 3.4 12.6 - - - +
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Residues in contact with ARG 563 (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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223B LEU* 2.6 34.2 + - - +
224B GLY* 4.2 1.4 - - - -
226B ASN* 5.2 2.6 + - - -
239B GLY* 3.7 23.7 - - - +
240B PHE 4.1 5.7 + - - +
241B PRO* 3.5 35.4 - - + +
244B GLU* 4.9 0.2 - - - +
503D ARG* 3.8 19.8 + - - +
505D GLU* 2.8 25.9 + - - +
506D GLU* 3.0 32.3 + - - +
559D LEU* 2.9 44.2 + - - +
560D ARG 4.0 4.9 - - - +
561D GLN 3.2 0.8 - - - -
562D ILE* 1.3 76.9 - - + +
564D GLN* 1.3 66.3 + - - +
565D GLY 3.6 1.4 - - - +
570D ARG* 3.4 16.8 + - - +
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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