Contacts of the helix formed by residues 2724 - 2729 (chain A) in PDB entry 5NUG
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 SER2724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2306A ASP* 5.0 5.2 + - - -
2346A GLN* 3.4 22.0 + - - -
2675A GLY 6.2 0.2 - - - -
2676A THR* 6.1 3.8 - - - -
2677A GLN* 4.5 4.8 - - - +
2680A ILE* 4.8 7.6 - - - +
2722A PRO 3.8 1.2 + - - -
2723A LEU* 1.3 74.1 - - - +
2725A HIS* 1.3 69.9 + - - +
2726A ARG* 3.6 10.2 + - - +
2727A PHE* 3.1 13.4 + - - +
2728A LEU* 3.0 19.4 + - - +
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Residues in contact with HIS2725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2226A SER* 4.1 12.2 + - - -
2346A GLN* 3.7 19.4 + - - +
2448A ASP* 3.5 42.2 + - + +
2450A THR* 3.9 23.7 + - - +
2723A LEU 3.7 4.3 + - - -
2724A SER* 1.3 72.5 + - - +
2726A ARG* 1.3 55.7 + - - +
2728A LEU* 3.0 12.1 + - + +
2729A ARG* 2.6 36.9 + - - +
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Residues in contact with ARG2726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2226A SER* 4.1 11.9 - - - +
2230A LYS* 3.4 12.6 - - - +
2304A ASP* 3.2 12.1 + - - -
2305A GLY* 3.1 47.5 + - - +
2306A ASP* 3.9 7.0 + - - +
2344A GLU* 3.3 11.5 + - - -
2345A VAL* 3.8 1.4 - - - +
2346A GLN* 3.6 51.6 - - + +
2684A ARG* 2.9 43.8 + - - +
2724A SER* 3.1 6.8 + - - +
2725A HIS* 1.3 78.2 - - - +
2727A PHE* 1.3 59.8 + - - +
2729A ARG* 3.7 9.9 - - - +
2730A HIS* 3.8 4.0 - - - -
4802A ATP 3.2 33.1 + - - +
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Residues in contact with PHE2727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2590A PRO* 5.9 1.3 - - + -
2592A VAL* 4.6 4.0 - - + -
2666A ILE* 4.0 14.4 - - + -
2680A ILE* 3.4 30.7 - - + -
2681A SER* 6.0 0.2 - - - -
2683A ILE* 3.4 38.6 - - + -
2684A ARG* 4.1 26.1 - - + +
2687A VAL* 5.1 8.7 - - + -
2708A PHE* 6.1 3.1 - - + -
2723A LEU* 3.9 34.5 - - + -
2724A SER* 3.1 9.3 + - - +
2726A ARG* 1.3 76.8 - - - +
2728A LEU* 1.3 69.8 + - - +
2729A ARG 3.3 0.3 + - - -
2730A HIS* 3.5 13.0 + - - +
2731A VAL* 3.4 30.1 + - + +
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Residues in contact with LEU2728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2447A MET* 3.6 31.0 - - + -
2448A ASP 4.2 5.2 - - - +
2453A ARG* 3.5 38.3 - - - +
2592A VAL* 5.0 4.3 - - + -
2723A LEU* 3.7 39.0 - - + +
2724A SER 3.0 11.1 + - - +
2725A HIS* 3.4 16.6 - - + +
2727A PHE* 1.3 77.2 - - + +
2729A ARG* 1.3 54.9 + - - +
2731A VAL* 2.5 53.1 + - + +
2733A VAL* 5.2 2.2 - - + -
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Residues in contact with ARG2729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2226A SER* 3.3 23.8 - - - +
2227A GLY 4.4 0.4 - - - +
2452A LEU* 3.6 52.0 - - + +
2453A ARG* 3.9 9.9 - - - +
2456A GLY* 5.7 0.7 - - - -
2688A GLU* 3.5 5.9 + - - -
2725A HIS 2.6 15.5 + - - +
2726A ARG 3.7 7.6 - - - +
2728A LEU* 1.3 71.0 - - - +
2730A HIS* 1.3 93.8 + - - +
2731A VAL 3.2 0.5 + - - -
4802A ATP 2.4 96.1 + - - -
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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