Contacts of the strand formed by residues 44 - 52 (chain K) in PDB entry 2VTX
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 GLN 44 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32K PHE* 6.0 0.2 - - - -
42K GLU 5.3 1.6 - - - +
43K HIS* 1.3 75.3 - - - +
45K LEU* 1.3 60.1 + - - +
95K GLU* 3.6 33.0 + - + +
96K LEU 3.5 10.4 - - - +
97K ASP* 2.7 45.0 + - - +
98K PRO* 4.3 1.1 - - - -
117K HIS* 3.4 8.3 - - - +
118K VAL* 3.0 45.3 + - + +
119K ALA 4.1 15.3 - - - +
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Residues in contact with LEU 45 (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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19K TRP* 3.8 45.5 - - + -
32K PHE* 4.0 44.0 - - + -
44K GLN* 1.3 71.9 - - - +
46K ALA* 1.3 59.3 + - - +
47K LEU* 4.0 16.7 + - + -
94K ILE 3.6 1.9 - - - +
95K GLU* 3.4 2.1 - - - -
96K LEU* 2.8 46.0 + - + +
98K PRO* 4.7 1.6 - - + +
100K VAL* 4.5 14.1 - - + -
102K PHE* 4.5 2.0 - - + -
115K GLY 4.4 0.2 - - - -
116K GLN 3.7 25.6 - - - +
117K HIS* 4.4 4.7 - - + +
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Residues in contact with ALA 46 (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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44K GLN 3.9 1.2 + - - -
45K LEU* 1.3 72.9 - - - +
47K LEU* 1.3 62.2 + - - +
48K ARG* 3.4 34.8 - - - +
94K ILE 3.2 8.7 - - - +
95K GLU* 4.2 11.0 - - + +
115K GLY* 3.1 3.7 - - - -
116K GLN 2.9 33.7 + - - +
118K VAL* 4.0 16.2 - - + -
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Residues in contact with LEU 47 (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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19K TRP* 4.4 2.0 - - + -
45K LEU* 4.0 18.6 + - + -
46K ALA* 1.3 76.0 - - - +
48K ARG* 1.3 72.5 + - - +
49K THR 5.0 0.2 - - - +
50K VAL* 5.5 1.1 - - + -
78K ILE* 3.7 30.3 - - + -
91K MET* 3.6 34.0 - - + +
93K GLY 5.4 0.9 + - - -
94K ILE* 3.0 26.4 + - + +
96K LEU* 4.4 14.4 - - + -
102K PHE* 3.8 33.0 - - + -
113K ILE* 4.0 22.2 - - + -
114K SER 3.5 5.8 - - - +
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Residues in contact with ARG 48 (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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92G VAL 3.7 18.4 + - - +
93G GLY* 2.9 26.0 + - - -
94G ILE* 3.7 25.1 - - + -
18K ILE* 5.6 1.3 - - + -
46K ALA* 3.4 32.4 - - - +
47K LEU* 1.3 82.9 + - - +
49K THR* 1.3 68.4 + - + +
90K THR* 3.7 5.7 - - - +
91K MET* 3.0 27.4 + - - +
93K GLY 5.8 3.8 - - - +
114K SER* 2.8 23.2 + - - +
115K GLY* 3.9 18.4 - - - +
116K GLN* 2.9 30.3 + - + +
118K VAL* 5.1 9.3 - - - +
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Residues in contact with THR 49 (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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77G PRO 4.3 0.9 + - - -
78G ILE* 2.9 34.1 + - - +
91G MET* 4.2 15.5 - - + -
92G VAL 6.1 0.2 - - - +
94G ILE* 4.2 15.3 - - + -
47K LEU* 5.7 0.2 - - - +
48K ARG* 1.3 94.5 - - + +
50K VAL* 1.3 62.4 + - - +
51K CYS* 4.2 1.2 - - - -
88K MET* 4.5 5.4 - - + -
89K ALA 3.4 11.4 - - - +
90K THR* 4.8 4.9 - - + +
91K MET* 4.4 3.3 - - - +
113K ILE* 3.5 2.3 - - - +
114K SER* 2.7 47.2 + - - +
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Residues in contact with VAL 50 (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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47K LEU* 5.5 0.2 - - + -
49K THR* 1.3 76.7 - - - +
51K CYS* 1.3 68.4 + - - +
63K VAL* 4.4 20.0 - - + -
78K ILE* 5.4 3.1 - - + -
79K ALA* 4.8 1.8 - - + -
81K LEU* 3.4 22.4 - - + -
88K MET* 3.2 1.7 - - - +
89K ALA 2.9 31.2 + - - +
91K MET* 3.8 30.5 - - + -
111K LEU* 3.6 22.4 - - + -
112K TYR 3.2 12.8 - - - +
113K ILE* 4.6 15.3 - - + -
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Residues in contact with CYS 51 (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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77G PRO* 4.2 15.9 - - - -
78G ILE 3.9 6.7 - - - +
79G ALA* 3.8 24.2 - - - -
80G THR* 3.6 18.6 - - - +
49K THR* 4.7 1.8 - - - -
50K VAL* 1.3 78.7 - - - +
52K LEU* 1.3 64.4 + - - +
81K LEU* 4.2 2.7 - - - -
87K PRO 3.5 6.1 - - - -
88K MET* 3.3 18.6 - - + +
111K LEU* 3.7 3.5 - - - +
112K TYR* 2.9 44.9 + - - +
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Residues in contact with LEU 52 (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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62G ILE* 3.9 1.0 - - - +
80G THR* 2.7 30.6 + - + +
51K CYS* 1.3 80.8 - - - +
53K GLY* 1.3 69.9 + - - +
56K ALA* 4.4 2.2 - - + -
61K HIS* 4.1 28.9 - - + +
81K LEU* 4.0 17.5 - - + -
82K LYS* 3.7 14.8 - - - +
83K PRO* 3.4 46.2 - - + -
87K PRO* 3.1 21.8 + - + +
110K PRO 3.9 4.3 - - - +
111K LEU* 4.1 13.7 - - + -
112K TYR* 4.1 3.1 - - - -
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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