Contacts of the helix formed by residues 2617 - 2632 (chain A) in PDB entry 5NP1
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 VAL2617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2615A GLN* 2.8 23.4 - - + +
2616A MET* 1.3 75.9 - - - +
2618A ARG* 1.3 49.0 - - - +
2619A SER* 2.8 9.5 - - - -
2620A VAL* 2.2 40.0 + - + +
2665A PRO* 3.7 29.1 - - + +
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Residues in contact with ARG2618 (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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2616A MET* 2.8 8.3 - - - -
2617A VAL* 1.3 77.3 - - - +
2619A SER* 1.3 50.6 - - - +
2620A VAL 3.0 0.4 - - - -
2621A GLU* 2.8 21.7 + - + +
2622A ALA* 2.5 32.7 + - - +
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Residues in contact with SER2619 (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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2616A MET 3.9 7.5 + - - -
2617A VAL* 3.7 5.4 - - - -
2618A ARG* 1.3 75.6 - - - +
2620A VAL* 1.3 49.4 + - - -
2622A ALA* 2.7 14.2 + - - +
2623A LEU* 2.3 36.7 + - - +
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Residues in contact with VAL2620 (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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2617A VAL* 2.2 31.5 + - + +
2619A SER* 1.3 69.2 - - - +
2621A GLU* 1.3 50.2 + - - +
2623A LEU* 2.8 12.2 + - - +
2624A CYS* 2.4 36.1 + - - +
2664A VAL* 6.4 0.9 - - + -
2665A PRO* 4.2 27.8 - - + +
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Residues in contact with GLU2621 (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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2561A LEU* 5.0 16.3 - - + +
2565A ASN* 6.1 4.0 - - + -
2617A VAL 3.7 0.2 + - - -
2618A ARG* 2.8 30.4 + - + +
2620A VAL* 1.3 74.8 - - - +
2622A ALA* 1.3 47.8 - - - -
2624A CYS* 2.9 11.7 + - + +
2625A ASP* 2.2 38.8 + - - +
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Residues in contact with ALA2622 (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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2618A ARG 2.5 16.0 + - - +
2619A SER* 2.7 18.9 + - - +
2621A GLU* 1.3 70.2 - - - +
2623A LEU* 1.3 47.0 + - - -
2625A ASP* 3.0 11.7 - - + +
2626A ALA* 2.1 40.4 + - - +
2658A ASN* 6.2 0.7 - - - -
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Residues in contact with LEU2623 (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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2619A SER 2.3 25.0 + - - +
2620A VAL* 2.8 18.8 + - - +
2622A ALA* 1.3 65.8 - - - +
2624A CYS* 1.3 48.2 + - - -
2626A ALA* 3.2 8.7 - - - +
2627A TYR* 2.2 39.1 + - - +
2658A ASN* 5.5 7.2 - - + -
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Residues in contact with CYS2624 (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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2561A LEU* 6.0 4.0 - - + -
2565A ASN* 5.6 9.6 - - + -
2620A VAL 2.4 26.2 + - - +
2621A GLU* 3.0 17.0 - - + +
2623A LEU* 1.3 66.8 - - - +
2625A ASP* 1.3 46.0 - - - -
2627A TYR* 2.8 11.9 + - - +
2628A ILE* 2.0 41.1 + - - +
2760A LEU* 5.2 14.8 - - + -
2765A GLY 6.1 0.2 - - - +
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Residues in contact with ASP2625 (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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2621A GLU 2.2 27.5 + - - +
2622A ALA* 3.1 16.8 - - + +
2624A CYS* 1.3 67.2 - - - +
2626A ALA* 1.3 47.8 + - - +
2628A ILE* 2.8 11.3 + - + +
2629A ILE* 2.1 37.5 + - - +
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Residues in contact with ALA2626 (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 ALA 2.1 29.4 + - - +
2623A LEU* 3.2 11.4 - - - +
2625A ASP* 1.3 65.0 - - - +
2627A TYR* 1.3 53.6 + - - +
2628A ILE 2.9 0.7 - - - -
2629A ILE* 2.8 11.8 + - - +
2630A LEU* 2.2 36.0 + - - +
2654A THR* 3.2 35.5 - - - +
2655A LYS* 5.5 0.4 - - + -
2658A ASN* 4.4 8.7 - - + -
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Residues in contact with TYR2627 (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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2623A LEU 2.2 28.4 + - - +
2624A CYS* 3.0 15.0 - - - +
2626A ALA* 1.3 66.8 - - - +
2628A ILE* 1.3 49.4 + - - +
2630A LEU* 2.9 14.4 - - + +
2631A ALA* 2.3 31.9 + - - +
2765A GLY* 5.1 17.7 - - - +
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Residues in contact with ILE2628 (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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2570A GLU* 6.5 1.6 - - + -
2624A CYS 2.0 27.6 + - - +
2625A ASP* 3.1 17.3 - - - +
2627A TYR* 1.3 65.0 - - - +
2629A ILE* 1.3 60.1 + - - +
2631A ALA* 2.6 31.8 + - + +
2632A ASN* 2.9 9.9 + - - +
2761A SER* 5.7 6.1 - - - -
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Residues in contact with ILE2629 (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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2625A ASP 2.1 28.0 + - - +
2626A ALA* 3.1 10.8 - - - +
2628A ILE* 1.3 66.7 - - - +
2630A LEU* 1.3 54.8 + - - +
2632A ASN* 2.7 30.7 + - - +
2633A LEU* 3.5 1.9 + - - -
2653A ILE* 5.3 5.4 - - + +
2654A THR* 3.4 29.8 - - - +
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Residues in contact with LEU2630 (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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2626A ALA 2.2 26.8 + - - +
2627A TYR* 2.9 18.2 - - - +
2629A ILE* 1.3 65.1 - - - +
2631A ALA* 1.3 53.4 + - - +
2632A ASN 2.8 4.9 - - - -
2633A LEU* 2.5 40.0 + - + +
2654A THR* 4.1 6.8 - - - -
2700A LYS* 5.3 6.7 - - + +
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Residues in contact with ALA2631 (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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2627A TYR 2.3 20.2 + - - +
2628A ILE* 2.6 27.7 + - + +
2630A LEU* 1.3 67.5 - - - +
2632A ASN* 1.3 56.1 + - - -
2633A LEU 3.2 3.6 + - - +
2718A GLY* 5.4 6.9 - - - -
2761A SER* 5.2 3.8 - - - -
2763A ARG* 5.8 2.0 - - + -
2764A SER* 4.0 27.6 - - - -
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Residues in contact with ASN2632 (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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2570A GLU 6.0 2.2 - - - +
2628A ILE 2.9 4.6 + - - +
2629A ILE* 2.7 19.2 + - - +
2631A ALA* 1.3 76.6 - - - +
2633A LEU* 1.3 66.4 + - - +
2634A ASP* 3.1 11.7 + - - +
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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