Contacts of the helix formed by residues 627 - 633 (chain E) in PDB entry 4E3C
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 PRO 627 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623E LEU 3.5 14.4 - - - +
624E GLU* 3.5 14.1 - - - +
626E LEU* 1.4 93.0 - - + +
628E LYS* 1.3 56.4 + - + +
629E VAL 3.0 5.8 - - - -
630E GLU* 2.8 37.7 + - + +
631E GLU* 3.0 21.2 + - - +
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Residues in contact with LYS 628 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529E GLU* 5.9 0.7 - - - -
533E LEU* 3.6 27.1 - - + +
536E ARG* 4.7 14.5 - - - +
624E GLU 4.6 9.9 - - - +
625E LEU* 4.5 20.2 - - + +
626E LEU 3.4 0.8 - - - -
627E PRO* 1.3 82.7 - - - +
629E VAL* 1.3 60.7 + - + +
631E GLU* 3.9 11.9 - - - +
632E VAL* 3.0 27.8 - - + +
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Residues in contact with VAL 629 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470E ASN* 6.0 7.2 - - + -
530E VAL* 5.8 1.3 - - + -
533E LEU* 3.7 41.1 - - + -
536E ARG* 5.0 6.1 - - - +
537E MET* 5.3 9.0 - - + -
625E LEU 3.9 16.2 - - - +
626E LEU* 2.9 22.4 - - + +
627E PRO 3.0 0.4 - - - -
628E LYS* 1.3 81.1 - - + +
630E GLU* 1.3 59.8 + - - +
631E GLU 3.5 0.7 - - - -
632E VAL* 4.2 2.5 - - - -
633E VAL* 3.0 33.4 - - + +
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Residues in contact with GLU 630 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626E LEU* 3.1 19.7 + - + +
627E PRO* 2.8 34.0 + - + +
629E VAL* 1.3 79.5 - - - +
631E GLU* 1.3 60.8 + - - +
633E VAL* 3.2 19.0 - - - +
634E SER* 3.3 13.0 - - - -
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Residues in contact with GLU 631 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627E PRO 3.0 16.0 + - - +
628E LYS* 3.9 14.2 - - - +
630E GLU* 1.3 77.9 - - - +
632E VAL* 1.3 72.1 + - - +
633E VAL 3.3 0.2 - - - -
634E SER* 2.9 7.8 + - - -
635E LEU* 2.7 61.0 + - + +
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Residues in contact with VAL 632 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526E ARG* 3.6 5.3 - - + -
529E GLU* 3.3 36.3 - - + +
530E VAL* 3.3 30.3 - - + +
533E LEU* 3.6 11.4 - - + -
628E LYS* 3.0 24.8 + - + +
629E VAL* 4.5 1.6 - - - -
630E GLU 3.6 0.2 - - - -
631E GLU* 1.3 89.8 - - - +
633E VAL* 1.3 60.1 + - + +
635E LEU* 3.4 22.9 + - + +
636E MET* 3.5 12.5 - - - +
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Residues in contact with VAL 633 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E ALA* 3.4 33.2 - - + -
475E MET* 5.3 0.3 - - - +
530E VAL* 3.5 22.2 - - + -
629E VAL* 3.0 26.9 + - + +
630E GLU* 3.2 14.4 - - + +
632E VAL* 1.3 76.3 - - - +
634E SER* 1.3 65.0 + - - +
636E MET* 3.4 34.2 - - + +
637E ASN* 3.8 11.1 + - - -
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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