Contacts of the strand formed by residues 42 - 52 (chain A) in PDB entry 2VNE
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 VAL 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A THR* 1.3 74.8 - - - +
43A THR* 1.3 70.1 + - - +
44A LYS* 5.1 5.4 - - + -
162A HIS* 3.6 2.8 - - - -
163A VAL* 2.8 45.2 + - + +
165A PRO* 4.6 12.3 - - + +
168A VAL* 4.0 23.1 - - + -
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Residues in contact with THR 43 (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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42A VAL* 1.3 81.8 - - - +
44A LYS* 1.3 68.6 + - - +
45A VAL* 4.0 13.0 - - + -
160A GLU* 3.4 37.0 + - + +
161A TYR 3.5 4.0 - - - -
162A HIS* 3.3 19.4 + - + +
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Residues in contact with LYS 44 (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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42A VAL* 3.7 6.9 + - + +
43A THR* 1.3 78.3 - - - +
45A VAL* 1.3 63.9 + - - +
46A ILE* 4.2 19.2 - - - +
159A THR 3.7 1.6 - - - +
160A GLU* 3.4 3.1 - - - -
161A TYR* 2.9 71.9 + - + +
163A VAL* 4.9 7.2 - - + -
168A VAL* 5.5 8.5 - - + -
172A GLU* 3.1 38.9 + - + +
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Residues in contact with VAL 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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43A THR* 4.0 17.9 - - + -
44A LYS* 1.3 81.2 - - - +
46A ILE* 1.3 71.8 + - - +
47A HIS* 3.3 36.7 - - + +
158A SER* 4.6 6.5 - - - +
159A THR 3.4 9.0 - - - +
160A GLU* 4.2 15.7 - - + +
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Residues in contact with ILE 46 (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 LYS* 4.2 21.3 - - - +
45A VAL* 1.3 80.7 - - - +
47A HIS* 1.3 65.2 + - - +
158A SER* 3.2 4.7 - - - -
159A THR* 3.0 52.9 + - + +
161A TYR* 4.9 7.9 - - + -
175A ILE* 3.4 35.9 - - + +
176A THR* 3.8 22.4 - - - +
177A THR* 4.1 8.5 + - - +
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Residues in contact with HIS 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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45A VAL* 3.3 32.4 - - + +
46A ILE* 1.3 79.7 - - - +
48A HIS* 1.3 63.3 + - - +
49A GLU* 5.5 6.7 - - + +
157A SER 3.5 3.4 - - - +
158A SER* 3.6 16.1 - - - -
177A THR* 3.7 11.2 + - - +
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Residues in contact with HIS 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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47A HIS* 1.3 72.5 - - - +
49A GLU* 1.3 77.4 + - - +
50A LEU* 3.9 30.7 - - + +
155A ILE 3.4 1.8 - - - +
156A LYS* 3.5 3.5 - - - +
157A SER* 2.7 52.1 + - - +
177A THR* 3.1 33.6 - - + +
180A LEU* 4.3 1.1 - - + -
181A ALA* 3.4 40.3 + - + +
184A ALA* 4.7 2.0 - - + +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A HIS* 5.5 5.8 - - + +
48A HIS* 1.3 91.4 + - - +
50A LEU* 1.3 63.0 + - - +
51A GLU* 3.8 2.5 + - + -
154A VAL* 3.2 23.5 - - + +
155A ILE 3.5 3.6 - - - -
156A LYS* 3.5 36.4 - - + +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A HIS* 3.9 23.5 + - + +
49A GLU* 1.3 73.9 - - - +
51A GLU* 1.3 66.3 + - - +
52A VAL* 3.6 15.5 + - + +
154A VAL* 4.3 0.7 - - - -
155A ILE* 2.9 39.6 + - + +
181A ALA 5.2 0.9 - - - +
184A ALA* 3.8 37.7 - - + -
185A ASP* 3.8 16.8 - - + +
188A SER* 3.8 15.7 - - - +
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Residues in contact with GLU 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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49A GLU 3.8 4.2 + - - -
50A LEU* 1.3 74.7 - - - +
52A VAL* 1.3 63.2 + - - +
148A THR* 3.0 32.8 - - - +
152A SER* 4.3 5.4 + - - -
153A CYS 3.3 20.2 - - - +
154A VAL* 3.8 17.9 - - + +
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Residues in contact with VAL 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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50A LEU* 3.8 22.0 - - + +
51A GLU* 1.3 78.9 - - - +
53A ALA* 1.3 58.9 + - - +
54A ALA* 3.2 7.0 + - + +
59A ILE* 4.3 10.1 - - + -
152A SER* 3.3 6.4 - - - -
153A CYS* 2.9 51.1 + - - +
155A ILE* 4.1 11.4 - - + -
188A SER* 3.3 33.2 - - - +
192A LEU* 5.0 9.2 - - + -
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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