Contacts of the helix formed by residues 625 - 632 (chain F) in PDB entry 1EJH
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 625 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624F TYR* 1.3 74.0 - - - +
626F ARG* 1.3 82.8 + - - +
627F GLU* 3.0 22.8 + - - +
628F PHE* 3.2 15.3 + - + +
629F LEU* 3.1 20.8 + - - +
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Residues in contact with ARG 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLU* 2.8 38.0 + - - +
135B LEU* 4.6 5.6 - - + +
186B ARG* 3.6 30.3 - - - +
624F TYR 3.8 1.6 + - - -
625F ASP* 1.3 77.6 + - - +
627F GLU* 1.3 63.2 + - + +
629F LEU* 3.7 9.6 - - - +
630F LEU* 2.9 62.5 + - + +
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Residues in contact with GLU 627 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625F ASP* 3.0 15.8 + - - +
626F ARG* 1.3 80.2 - - + +
628F PHE* 1.3 66.9 + - - +
630F LEU* 3.2 8.3 + - - +
631F ASP* 2.9 31.8 + - - +
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Residues in contact with PHE 628 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B HIS* 3.6 36.1 - + + -
69B VAL* 4.5 2.9 - - + -
624F TYR* 3.4 36.6 - + - -
625F ASP* 3.2 24.1 + - + +
627F GLU* 1.3 77.5 - - - +
629F LEU* 1.3 68.3 + - + +
631F ASP* 3.1 24.5 + - + +
632F PHE* 3.7 31.4 - + - -
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Residues in contact with LEU 629 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 5.0 0.2 - - + -
69B VAL* 3.7 31.6 - - + -
73B TRP* 2.8 27.5 + - + +
135B LEU* 3.7 44.2 - - + +
138B ILE* 3.8 27.1 - - + -
139B GLY* 4.0 9.6 - - - -
624F TYR* 3.6 25.4 - - + +
625F ASP 3.1 16.2 + - - +
626F ARG* 3.7 7.2 - - - +
628F PHE* 1.3 80.3 - - + +
630F LEU* 1.3 63.3 + - - +
632F PHE* 3.1 8.8 + - - +
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Residues in contact with LEU 630 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B TRP* 3.9 22.4 - - + -
131B LEU* 4.5 9.4 - - + -
135B LEU* 3.9 17.3 - - + -
626F ARG* 2.9 66.6 + - - +
627F GLU* 3.8 5.6 - - - +
629F LEU* 1.3 73.2 - - - +
631F ASP* 1.3 61.6 - - - +
633F GLN* 3.2 31.7 + - - +
634F PHE* 4.8 2.6 + - - -
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Residues in contact with ASP 631 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627F GLU* 2.9 22.8 + - - +
628F PHE* 3.1 14.8 + - + +
630F LEU* 1.3 77.4 - - - +
632F PHE* 1.3 65.2 + - + +
633F GLN 3.4 0.2 - - - -
634F PHE* 4.5 2.6 + - - +
635F MET* 3.5 26.2 - - + +
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Residues in contact with PHE 632 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TYR* 3.2 24.5 - - - -
37B HIS* 3.5 23.8 - + - -
69B VAL* 3.8 17.5 - - + -
70B GLU* 3.6 15.1 - - + -
73B TRP* 3.7 20.4 - - + +
628F PHE* 3.7 42.6 - + - -
629F LEU 3.1 8.6 + - - +
630F LEU 3.1 1.0 - - - -
631F ASP* 1.3 81.4 - - + +
633F GLN* 1.3 65.2 + - - +
634F PHE 3.1 4.2 + - - -
635F MET* 3.1 48.8 + - + +
636F PRO* 5.3 0.2 - - - +
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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