Contacts of the helix formed by residues 2677 - 2689 (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 GLN2677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2666A ILE 3.9 0.5 - - - +
2667A ASN 3.4 15.0 - - - +
2669A PRO* 3.0 34.1 - - + +
2670A ASP 4.0 9.6 - - - +
2671A MET* 3.8 22.6 - - + +
2675A GLY 5.3 0.2 - - - +
2676A THR* 1.3 75.3 - - - +
2678A ARG* 1.3 66.9 + - - +
2679A VAL 4.6 0.9 - - - +
2680A ILE* 3.8 33.2 - - + +
2681A SER* 3.1 22.4 + - - -
2721A LYS* 4.6 2.5 + - - -
2722A PRO 3.6 23.0 + - - -
2723A LEU* 3.9 13.5 - - - +
2724A SER* 4.5 3.6 - - - +
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Residues in contact with ARG2678 (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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2257A LYS* 3.2 27.5 + - + +
2258A ALA* 4.1 3.3 + - - -
2259A ILE* 4.3 6.2 - - - +
2260A SER* 4.0 30.9 - - - +
2263A HIS* 5.7 3.2 + - - -
2626A THR 5.6 0.4 - - - +
2627A THR* 3.7 29.8 - - + +
2628A PRO* 4.0 27.4 - - + +
2629A GLU* 5.6 5.5 + - - +
2669A PRO* 5.9 0.6 - - - +
2670A ASP 4.7 3.6 + - - -
2672A ASP* 4.6 20.1 + - - +
2676A THR 3.9 1.4 + - - -
2677A GLN* 1.3 71.9 - - - +
2679A VAL* 1.3 60.5 + - + +
2681A SER* 2.5 23.2 + - - -
2682A PHE* 2.9 16.3 + - - +
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Residues in contact with VAL2679 (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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2622A PHE* 3.2 38.6 - - + -
2626A THR* 3.6 18.2 - - + +
2627A THR* 3.3 43.7 - - - +
2628A PRO* 4.1 5.6 - - + -
2631A LEU* 4.2 13.9 - - + -
2669A PRO* 4.5 13.1 - - + +
2677A GLN* 3.4 1.0 - - - +
2678A ARG* 1.3 77.3 - - + +
2680A ILE* 1.3 59.4 + - + +
2682A PHE* 3.2 5.3 + - - +
2683A ILE* 2.9 28.8 + - + +
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Residues in contact with ILE2680 (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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2622A PHE* 5.0 0.7 - - + -
2666A ILE* 3.3 35.2 - - + +
2669A PRO* 5.1 2.2 - - + -
2677A GLN* 3.5 35.8 + - + +
2678A ARG 3.3 0.4 - - - -
2679A VAL* 1.3 86.2 - - + +
2681A SER* 1.3 56.4 + - - +
2683A ILE* 3.2 24.0 - - + +
2684A ARG* 2.9 27.1 + - - +
2723A LEU* 3.9 11.7 - - + -
2724A SER* 4.8 9.2 - - - +
2727A PHE* 3.4 37.6 - - + -
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Residues in contact with SER2681 (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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2255A ASP* 4.0 13.0 - - - +
2257A LYS* 3.2 21.3 - - - +
2258A ALA* 3.1 19.7 + - - -
2676A THR* 4.5 7.9 - - - -
2677A GLN 3.1 11.4 + - - -
2678A ARG 2.5 21.0 + - - -
2680A ILE* 1.3 76.2 - - - +
2682A PHE* 1.3 55.2 + - - +
2684A ARG* 3.2 13.0 + - - +
2685A GLN* 2.9 28.4 + - - +
2727A PHE* 6.0 0.2 - - - -
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Residues in contact with PHE2682 (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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2258A ALA* 3.3 36.8 - - + -
2259A ILE* 5.6 2.9 - - + -
2628A PRO* 3.5 27.1 - - + -
2631A LEU* 3.8 23.6 - - + -
2632A LEU* 3.5 31.2 - - + -
2635A PHE* 4.7 0.7 - + - -
2678A ARG 2.9 6.8 + - - +
2679A VAL* 3.2 9.6 - - - +
2681A SER* 1.3 76.1 + - - +
2683A ILE* 1.3 60.7 - - - +
2685A GLN* 3.2 5.6 + - - +
2686A MET* 2.9 58.8 + - + +
2692A PHE* 3.7 32.3 - + + -
2693A TYR 5.4 2.2 - - - -
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Residues in contact with ILE2683 (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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2622A PHE* 5.4 4.7 - - + -
2631A LEU* 3.6 31.0 - - + -
2663A CYS* 5.7 2.7 - - - -
2666A ILE* 4.9 10.8 - - + -
2679A VAL* 2.9 18.8 + - + +
2680A ILE* 3.2 31.9 - - + +
2682A PHE* 1.3 78.7 - - + +
2684A ARG* 1.3 57.3 + - - +
2686A MET* 3.2 6.6 + - - +
2687A VAL* 2.9 35.6 + - + +
2708A PHE* 4.1 33.0 - - + -
2727A PHE* 3.4 32.8 - - + -
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Residues in contact with ARG2684 (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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2255A ASP* 4.0 18.5 + - - +
2304A ASP* 2.5 33.9 + - - -
2680A ILE 2.9 13.9 + - - +
2681A SER* 3.3 11.2 - - - +
2683A ILE* 1.3 77.2 - - - +
2685A GLN* 1.3 59.4 + - - +
2687A VAL* 3.2 6.3 + - - +
2688A GLU* 2.9 57.5 + - + +
2689A HIS* 5.3 1.4 + - + -
2726A ARG* 2.9 59.0 + - - +
2727A PHE* 4.1 22.9 - - + +
2730A HIS* 3.9 7.9 + - + -
4802A ATP 3.5 18.4 + - - -
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Residues in contact with GLN2685 (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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2253A ILE 5.0 0.8 + - - -
2254A ILE* 4.3 1.4 - - - +
2255A ASP* 3.5 36.3 + - + +
2258A ALA* 3.7 18.7 - - + +
2259A ILE* 5.9 2.8 - - - +
2681A SER 2.9 12.3 + - - +
2682A PHE* 3.3 11.1 - - - +
2684A ARG* 1.3 77.9 - - - +
2686A MET* 1.3 62.3 + - - +
2689A HIS* 3.1 48.4 + - + +
2690A GLY 3.4 0.2 + - - -
2691A GLY 3.2 15.5 - - - +
2692A PHE* 3.2 30.1 - - - +
2693A TYR* 4.2 20.7 + - - -
2700A TRP* 4.6 3.0 - - + -
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Residues in contact with MET2686 (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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2631A LEU* 5.0 0.4 - - - -
2635A PHE* 3.4 20.0 - - + -
2682A PHE* 2.9 49.1 + - + +
2683A ILE* 3.4 9.9 - - - +
2685A GLN* 1.3 76.5 - - - +
2687A VAL* 1.3 57.3 + - - +
2690A GLY* 3.0 28.1 - - - -
2691A GLY 3.2 8.3 + - - +
2692A PHE* 4.0 14.1 - - + -
2703A LEU* 3.3 44.1 - - + +
2708A PHE* 3.4 36.3 - - + -
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Residues in contact with VAL2687 (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* 4.2 26.7 - - + -
2683A ILE* 2.9 20.4 + - + +
2684A ARG* 3.2 9.2 + - - +
2686A MET* 1.3 78.5 - - - +
2688A GLU* 1.3 66.9 + - - +
2690A GLY* 3.7 4.9 + - - -
2708A PHE* 4.3 20.4 - - + -
2727A PHE* 5.1 10.1 - - + -
2730A HIS* 3.5 34.8 - - + +
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Residues in contact with GLU2688 (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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2231A SER* 3.2 27.5 + - - -
2304A ASP* 3.4 4.4 - - - +
2684A ARG* 2.9 51.4 + - - +
2687A VAL* 1.3 77.3 - - - +
2689A HIS* 1.3 82.2 + - + +
2690A GLY* 4.6 0.3 - - - -
2729A ARG* 3.5 9.7 + - - -
2730A HIS* 3.6 34.8 - - + +
4802A ATP 4.1 1.1 + - - -
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Residues in contact with HIS2689 (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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2231A SER* 6.1 0.7 - - - -
2234A TRP* 5.7 1.8 - + - -
2235A ARG* 4.7 6.7 + - - +
2253A ILE* 3.8 35.9 - - + +
2254A ILE 6.1 0.9 - - - -
2255A ASP* 5.9 1.1 - - + -
2304A ASP* 3.1 41.4 + - - +
2344A GLU* 5.3 0.7 - - - -
2684A ARG* 4.9 2.2 + - - -
2685A GLN* 3.1 35.6 + - + +
2688A GLU* 1.3 96.5 + - + +
2690A GLY* 1.3 63.1 + - - +
2691A GLY 3.2 0.2 - - - -
2700A TRP* 3.2 29.4 + - + -
2702A LYS* 5.6 2.1 - - - -
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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