Contacts of the helix formed by residues 44 - 57 (chain A) in PDB entry 2VDY
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 SER 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 1.3 72.7 - - - +
45A PRO* 1.3 66.3 - - - +
46A VAL* 3.7 4.2 - - - +
47A SER* 3.2 31.7 + - - -
48A ILE* 3.2 17.3 + - - +
179A ILE* 3.4 14.8 - - - +
325A HIS* 3.1 15.6 + - - -
327A ALA* 5.4 0.4 - - - -
340A GLY* 4.8 1.3 - - - -
374A LEU 2.8 18.4 + - - -
375A PHE* 3.7 16.8 - - - -
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Residues in contact with PRO 45 (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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21A ASN 5.3 1.8 - - - +
24A PHE* 4.7 2.1 - - + -
25A ALA* 3.5 32.3 - - + -
28A LEU* 4.6 4.3 - - + -
43A ILE* 3.5 19.1 - - + +
44A SER* 1.3 83.6 - - - +
46A VAL* 1.3 56.6 + - - +
48A ILE* 3.1 14.2 + - + +
49A SER* 2.8 33.3 + - - -
373A SER* 3.6 21.8 - - - +
374A LEU 3.6 12.8 - - - +
376A LEU* 3.8 18.2 - - + +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 5.3 4.5 - - - +
44A SER* 3.7 11.9 - - - +
45A PRO* 1.3 77.8 - - - +
47A SER* 1.3 60.9 + - - +
49A SER* 3.8 5.2 - - - -
50A MET* 2.9 30.1 + - + +
87A PHE* 4.6 4.9 - - + -
90A LEU* 4.2 24.9 - - + -
94A PHE* 4.2 10.8 - - + -
105A MET* 3.8 20.0 - - + -
179A ILE* 4.1 5.6 - - + -
372A SER* 4.6 7.6 - - - -
373A SER 3.3 19.0 + - - +
374A LEU* 3.9 20.4 - - + -
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Residues in contact with SER 47 (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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44A SER* 3.2 26.6 + - - -
46A VAL* 1.3 82.1 - - - +
48A ILE* 1.3 56.5 + - - +
51A ALA* 3.1 30.5 + - - +
105A MET* 3.8 6.7 - - - -
177A ASN* 2.7 30.6 + - - +
179A ILE* 4.0 12.9 - - - +
325A HIS* 4.0 13.4 - - - -
341A ALA* 4.7 1.4 - - - -
342A MET* 4.3 10.8 + - - +
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Residues in contact with ILE 48 (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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24A PHE* 3.7 23.8 - - + -
28A LEU* 3.5 28.3 - - + -
43A ILE* 4.5 4.0 - - + -
44A SER 3.2 23.1 + - - +
45A PRO 3.1 5.9 + - - +
47A SER* 1.3 76.1 - - - +
49A SER* 1.3 62.1 + - - +
51A ALA* 3.5 1.0 + - - +
52A LEU* 3.1 41.2 + - + +
290A LEU* 4.0 17.7 - - + -
294A LEU* 5.5 0.4 - - + -
325A HIS* 4.0 21.1 - - + +
342A MET* 3.8 27.6 - - + -
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Residues in contact with SER 49 (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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21A ASN* 4.0 19.5 + - - +
24A PHE* 3.3 28.1 - - - +
45A PRO 2.8 18.8 + - - -
46A VAL* 3.8 7.0 - - - -
48A ILE* 1.3 73.6 - - - +
50A MET* 1.3 56.1 + - - +
52A LEU* 4.0 0.7 - - - +
53A ALA* 3.0 31.0 + - - +
71A LEU* 4.3 14.5 + - - +
73A PHE* 5.6 1.1 - - - -
87A PHE* 3.6 19.2 - - - -
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Residues in contact with MET 50 (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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46A VAL* 2.9 19.8 + - + +
47A SER 4.0 0.2 - - - +
49A SER* 1.3 73.2 - - - +
51A ALA* 1.3 60.2 + - - +
53A ALA* 4.5 0.2 - - - -
54A MET* 3.1 24.1 + - - +
87A PHE* 3.5 48.4 - - + +
90A LEU* 4.3 6.1 - - + -
91A HIS* 3.9 21.5 - - + +
105A MET* 3.9 25.6 - - + -
107A ASN* 3.6 21.9 - - - +
129A TYR* 3.5 23.9 - - + -
177A ASN* 3.6 20.0 - - - +
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Residues in contact with ALA 51 (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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47A SER 3.1 19.5 + - - +
48A ILE 3.9 1.1 - - - +
50A MET* 1.3 77.7 - - - +
52A LEU* 1.3 58.0 + - - +
54A MET* 3.4 6.7 + - - +
55A LEU* 3.1 24.8 + - - +
107A ASN* 4.9 1.3 - - - -
175A LEU* 3.7 19.6 - - + +
177A ASN* 3.7 21.3 - - + +
342A MET* 3.8 27.8 - - + -
344A LEU* 6.1 0.4 - - - +
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Residues in contact with LEU 52 (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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24A PHE* 4.3 0.9 - - + -
48A ILE* 3.1 35.7 + - + +
51A ALA* 1.3 74.7 - - - +
53A ALA* 1.3 60.5 + - - +
55A LEU* 3.4 20.9 + - + +
56A SER* 3.1 25.1 + - - -
67A LEU* 3.7 23.6 - - + +
71A LEU* 3.8 29.2 - - + +
294A LEU* 3.8 35.4 - - + -
299A ILE* 5.1 0.4 - - + -
302A LEU* 4.4 9.9 - - + -
323A VAL* 5.3 0.7 - - + -
342A MET* 4.9 10.8 - - + -
344A LEU* 4.4 10.5 - - + -
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Residues in contact with ALA 53 (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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49A SER 3.0 20.8 + - - +
50A MET 4.0 1.6 - - - +
52A LEU* 1.3 74.2 - - - +
54A MET* 1.3 63.8 + - - +
56A SER* 2.6 24.5 + - - -
57A LEU 3.7 0.2 + - - -
68A LEU* 5.7 0.7 - - + -
71A LEU* 4.0 11.1 - - + +
73A PHE* 4.8 0.7 - - + -
83A ILE* 4.3 10.3 - - + -
84A HIS* 3.1 13.7 - - - -
87A PHE* 3.6 19.1 - - + -
129A TYR* 3.3 17.7 - - - +
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Residues in contact with MET 54 (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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50A MET 3.1 18.5 + - - +
51A ALA* 3.5 7.9 - - - +
52A LEU 3.3 0.2 - - - -
53A ALA* 1.3 72.5 - - - +
55A LEU* 1.3 65.1 + - - +
57A LEU* 3.3 19.4 - - - +
107A ASN* 3.7 29.4 - - + +
108A ALA 4.5 7.6 - - - +
109A LEU* 4.7 6.7 - - + -
121A PHE* 4.2 8.3 - - + -
125A ILE* 3.9 22.9 - - + -
129A TYR* 3.6 38.1 + - + -
131A SER* 3.9 19.7 - - - +
175A LEU* 3.8 33.0 - - + -
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Residues in contact with LEU 55 (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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51A ALA 3.1 14.3 + - - +
52A LEU* 3.5 13.7 - - + +
53A ALA 3.3 0.2 - - - -
54A MET* 1.3 77.2 - - - +
56A SER* 1.3 53.4 + - - +
58A GLY* 2.8 28.8 + - - -
59A THR* 3.6 6.1 + - + +
67A LEU* 3.9 10.3 - - + -
121A PHE* 4.8 2.0 - - - -
173A LEU* 6.0 1.1 - - + -
175A LEU* 4.0 17.2 - - + +
302A LEU* 3.9 33.0 - - + -
309A PHE* 4.0 20.0 - - + -
312A ILE* 4.6 11.4 - - + +
344A LEU* 3.6 45.5 - - + -
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Residues in contact with SER 56 (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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52A LEU 3.1 13.4 + - - -
53A ALA* 2.6 22.5 + - - -
55A LEU* 1.3 74.9 - - - +
57A LEU* 1.3 58.6 + - - +
58A GLY 3.1 0.4 - - - -
59A THR* 2.8 25.7 + - - -
64A ARG* 4.0 1.3 - - - +
67A LEU* 3.8 15.0 - - - -
68A LEU* 3.6 30.1 - - - +
71A LEU* 5.3 0.2 - - - -
80A GLU* 3.5 12.8 + - - +
84A HIS* 3.6 2.8 - - - -
311A ARG* 2.9 16.8 + - - -
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Residues in contact with LEU 57 (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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54A MET 3.3 11.8 + - - +
56A SER* 1.3 80.2 + - - +
58A GLY* 1.3 56.6 + - - +
59A THR 3.4 0.2 - - - -
80A GLU* 4.0 5.8 - - - +
84A HIS* 3.5 32.1 - - + +
121A PHE* 3.8 15.8 - - + +
124A ASP* 3.7 45.5 - - + +
125A ILE* 4.0 14.8 - - + -
128A TYR* 4.9 2.2 - - + -
129A TYR* 3.9 27.1 - - + -
311A ARG* 3.1 36.1 + - - +
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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