Contacts of the helix formed by residues 93 - 103 (chain K) in PDB entry 4DVQ
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 93 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77K PRO* 3.6 29.8 - - + -
91K VAL* 5.0 0.2 - - - +
92K MET* 1.3 87.7 - - - +
94K PRO* 1.4 77.1 - - + +
95K GLU* 3.3 24.7 - - + +
96K ASP* 3.2 23.9 + - - +
97K VAL* 3.2 17.3 + - - +
393K GLN* 3.2 34.8 - - - +
410K LEU* 4.3 0.9 - - - -
413K ASN* 4.6 15.7 - - - +
416K LEU* 4.8 6.3 - - + -
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Residues in contact with PRO 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K MET 3.8 6.1 - - - +
93K LEU* 1.4 85.6 - - + +
95K GLU* 1.3 64.0 + - - +
97K VAL* 3.0 19.1 + - + +
98K GLU* 3.1 11.5 + - - +
410K LEU* 4.2 13.7 - - + +
416K LEU* 3.5 33.4 - - + -
417K PHE* 5.9 0.4 - - + -
438K PHE* 3.2 38.2 - - + +
439K HIS* 4.1 24.7 - - + +
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Residues in contact with GLU 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93K LEU* 3.9 32.1 - - + +
94K PRO* 1.3 81.6 - - - +
96K ASP* 1.3 70.6 + - - +
98K GLU* 3.4 12.8 + - - +
99K LYS* 3.1 29.8 + - + +
393K GLN* 4.6 7.5 + - - +
416K LEU* 5.2 5.0 - - - +
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Residues in contact with ASP 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77K PRO 4.1 6.1 - - - +
91K VAL* 3.8 31.1 - - + +
93K LEU* 3.2 20.7 + - - +
95K GLU* 1.3 75.7 - - - +
97K VAL* 1.3 60.9 + - - +
99K LYS* 3.2 3.2 + - - +
100K LEU* 2.9 26.8 + - - +
392K LEU* 3.1 33.3 - - + +
393K GLN* 3.0 48.1 + - - +
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Residues in contact with VAL 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K VAL* 5.3 0.2 - - + -
93K LEU 3.4 15.7 - - - +
94K PRO* 3.0 13.1 + - + +
96K ASP* 1.3 73.1 - - + +
98K GLU* 1.3 59.9 + - - +
100K LEU* 3.0 9.1 + - - +
101K GLN* 2.8 27.7 + - - +
382K LEU* 4.9 0.7 - - + -
405K VAL* 3.8 34.5 - - + -
410K LEU* 4.2 7.0 - - + -
438K PHE* 3.6 18.8 - - + -
441K VAL* 4.5 14.8 - - + -
445K PHE* 3.7 29.6 - - + -
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Residues in contact with GLU 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K PRO 3.1 8.9 + - - +
95K GLU* 3.6 14.5 - - - +
97K VAL* 1.3 74.4 - - - +
99K LYS* 1.3 53.5 + - + +
101K GLN* 3.1 3.1 + - - +
102K GLN* 2.8 50.8 + - - +
438K PHE* 3.6 43.7 - - + +
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Residues in contact with LYS 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K GLU* 3.1 17.9 + - - +
96K ASP* 3.4 3.6 - - - +
98K GLU* 1.3 79.4 - - + +
100K LEU* 1.3 59.2 + - - +
102K GLN* 3.1 27.4 - - + +
103K VAL* 3.4 15.1 - - - +
390K LEU* 3.5 5.4 - - + +
391K VAL* 3.1 40.9 + - - +
392K LEU* 3.4 24.9 - - + +
393K GLN 4.9 3.8 - - - +
394K ASN 5.5 1.0 - - - +
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Residues in contact with LEU 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K VAL* 5.7 0.2 - - + -
96K ASP 2.9 12.9 + - - +
97K VAL* 3.0 10.3 + - - +
99K LYS* 1.3 72.1 - - - +
101K GLN* 1.3 65.3 + - - +
102K GLN 3.1 1.1 - - - -
103K VAL* 3.0 14.9 + - - +
104K ASP* 3.2 11.3 + - - +
382K LEU* 5.9 1.6 - - + +
383K GLU 5.6 0.4 - - - -
384K ARG* 4.2 24.2 - - + +
386K VAL* 4.8 10.0 - - + +
390K LEU* 4.5 13.7 - - + -
392K LEU* 4.4 2.2 - - + +
403K VAL* 3.8 46.2 - - + +
405K VAL* 3.9 22.4 - - + -
445K PHE* 3.9 21.3 - - + -
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Residues in contact with GLN 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K VAL 2.8 14.1 + - - +
98K GLU 3.6 6.5 - - - +
100K LEU* 1.3 72.5 - - - +
102K GLN* 1.3 67.0 + - - +
104K ASP* 3.1 21.4 + - + +
438K PHE* 3.1 34.6 - - + -
445K PHE* 3.5 38.0 - - + +
446K GLY* 3.8 22.1 - - - +
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Residues in contact with GLN 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K GLU* 2.8 34.5 + - - +
99K LYS* 3.1 21.5 - - + +
100K LEU 3.1 0.4 - - - -
101K GLN* 1.3 77.7 - - - +
103K VAL* 1.3 60.7 + - + +
104K ASP 3.7 3.8 + - - +
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Residues in contact with VAL 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K LYS 3.4 15.7 - - - +
100K LEU 3.0 7.3 + - - +
102K GLN* 1.3 78.0 - - + +
104K ASP* 1.3 67.5 + - - +
105K SER* 3.3 2.6 + - - -
386K VAL* 3.6 27.3 - - + +
387K SER* 4.2 9.0 + - - -
388K SER* 3.5 36.6 + - - +
389K ASP 4.5 2.0 - - - +
390K LEU* 3.4 26.5 - - + -
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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