Contacts of the helix formed by residues 96 - 105 (chain A) in PDB entry 5V5Z
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 LEU 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 4.1 24.2 - - + +
76A ARG* 4.1 21.3 - - + -
80A GLY 4.5 0.2 - - - +
81A ASP* 2.9 33.1 + - - +
83A PHE* 3.5 30.5 - - + -
94A VAL* 4.2 10.1 - - + -
95A TYR* 1.3 88.5 - - - +
97A GLY* 1.3 68.0 + - - +
99A LYS* 4.4 0.7 + - - +
100A GLY 3.6 0.5 + - - -
405A SER* 4.9 7.6 - - - +
408A TYR* 3.5 50.3 - - + -
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Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASP* 5.2 0.7 - - - -
95A TYR 4.0 0.4 + - - -
96A LEU* 1.3 71.9 - - - +
98A PRO* 1.3 63.0 - - - -
99A LYS* 2.5 5.9 + - - -
100A GLY 2.5 31.4 + - - -
101A HIS* 3.1 16.6 + - - -
405A SER 5.6 2.6 + - - -
408A TYR* 4.6 4.9 - - - -
409A ALA* 4.5 11.6 - - - +
415A TYR* 3.4 16.2 - - - -
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Residues in contact with PRO 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLY* 1.3 80.8 - - - +
99A LYS* 1.3 63.9 + - + +
101A HIS* 3.4 18.3 - - - +
102A GLU* 3.3 16.8 + - - +
409A ALA* 5.2 0.4 - - + -
415A TYR* 3.1 35.9 - - + +
457A SER* 2.9 43.3 + - - +
459A PRO* 4.2 17.0 - - + -
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Residues in contact with LYS 99 (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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81A ASP* 4.5 17.4 + - - +
95A TYR* 3.1 31.7 + - + +
96A LEU 4.8 1.1 - - - +
97A GLY 2.5 6.4 + - - +
98A PRO* 1.3 79.4 - - + +
100A GLY* 1.3 62.8 + - - +
101A HIS 3.2 0.2 - - - -
102A GLU* 3.4 7.6 + - - +
103A PHE* 3.1 21.5 + - - +
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.2 46.0 - - - +
97A GLY 2.5 11.6 + - - -
99A LYS* 1.3 70.1 - - - +
101A HIS* 1.3 63.5 + - - -
103A PHE* 3.0 10.2 + - - +
104A VAL* 3.1 14.2 + - - +
404A VAL* 3.4 12.8 - - - +
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Residues in contact with HIS 101 (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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97A GLY* 3.1 14.9 + - - -
98A PRO* 3.4 19.9 - - + +
100A GLY* 1.3 75.1 - - - +
102A GLU* 1.3 63.1 + - - +
105A PHE* 3.0 41.6 + + + +
404A VAL* 3.5 22.0 - - + -
405A SER 4.4 2.3 + - - -
406A PRO* 3.4 28.9 - - + +
409A ALA* 4.6 5.0 - - + +
456A VAL* 3.2 21.9 + - + +
458A SER 3.0 28.9 + - - -
459A PRO* 3.5 20.2 - - + -
461A LEU* 4.2 4.8 - - + +
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Residues in contact with GLU 102 (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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98A PRO 3.3 6.4 + - - +
99A LYS* 3.8 8.5 - - - +
100A GLY 3.3 0.2 - - - -
101A HIS* 1.3 78.9 - - - +
103A PHE* 1.3 63.2 + - - +
106A ASN* 3.4 42.4 + - - +
454A LYS 4.0 2.1 - - - +
455A GLY* 4.8 0.5 - - - -
456A VAL* 3.1 36.4 + - + +
457A SER* 3.3 23.6 + - - +
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Residues in contact with PHE 103 (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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93A THR* 5.7 2.0 - - + -
95A TYR* 3.8 28.0 - + + -
99A LYS 3.1 15.7 + - - +
100A GLY 3.0 5.8 + - - +
102A GLU* 1.3 80.3 - - - +
104A VAL* 1.3 63.2 + - + +
107A ALA* 3.7 18.0 + - - +
112A VAL* 5.6 0.2 - - - +
387A LEU* 3.5 36.3 - - + +
388A ARG 4.0 7.6 - - - -
389A ILE* 4.1 22.0 - - + -
390A PRO* 3.8 29.6 - - + -
396A VAL* 4.5 4.7 - - + -
402A VAL* 3.4 31.0 - - + -
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Residues in contact with VAL 104 (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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95A TYR* 6.0 2.0 - - + -
100A GLY 3.1 5.1 + - - +
103A PHE* 1.3 83.2 - - + +
105A PHE* 1.3 68.3 + - - +
106A ASN 3.0 3.0 + - - -
107A ALA* 3.1 17.6 + - - +
112A VAL* 5.0 1.6 - - + +
379A ILE* 4.6 7.6 - - + +
381A ARG* 3.9 33.4 + - + +
402A VAL* 3.4 41.3 - - + -
403A LEU 4.1 8.3 - - - +
404A VAL* 3.8 36.1 - - + +
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Residues in contact with PHE 105 (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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101A HIS* 3.0 27.9 + + - +
104A VAL* 1.3 79.6 - - - +
106A ASN* 1.3 57.6 + - - +
107A ALA 5.1 1.1 - - - +
379A ILE* 3.5 32.3 - - + -
381A ARG* 3.8 12.5 + - - +
404A VAL* 3.5 22.2 - - + -
406A PRO* 3.9 14.8 - - + -
456A VAL* 3.7 13.5 - - + -
461A LEU* 3.5 31.2 - - + -
464A GLY* 3.6 15.5 - - - -
465A GLY 3.3 17.1 - - - +
466A GLY* 3.3 23.7 - - - -
467A ARG* 4.4 2.8 + - - +
468A HIS* 5.9 1.0 - - - -
601A HEM 3.6 17.5 - - - -
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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