Contacts of the strand formed by residues 21 - 25 (chain D) in PDB entry 1EV2
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 LYS 21 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D HIS 3.1 29.3 + - - +
17D PHE* 4.8 9.4 - - - +
19D ASP* 3.3 18.7 + - - +
20D PRO* 1.3 75.8 + - - +
22D ARG* 1.3 67.7 + - - +
23D LEU* 5.5 2.7 - - + -
51D ILE 3.5 0.2 - - - +
52D LYS* 4.8 0.2 - - - -
53D LEU* 2.7 43.6 + - - +
55D LEU* 5.2 18.3 - - + +
141D PRO* 4.4 20.6 - - + -
142D MET 3.3 20.4 - - - +
143D SER* 4.9 2.3 - - - +
144D ALA* 4.2 5.1 - - - +
283H ASP 5.6 5.2 - - - -
285H GLN* 5.1 9.2 - - - +
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Residues in contact with ARG 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 1.3 77.8 - - - +
23D LEU* 1.3 61.5 + - - +
24D TYR 3.8 0.4 + - - -
31D PHE* 3.9 28.6 - - + -
46D LYS* 3.3 31.0 + - - +
47D SER 5.7 0.2 - - - -
48D ASP 4.6 2.8 + - - -
51D ILE* 3.5 42.6 - - + +
52D LYS* 4.9 7.5 - - - +
140D LEU 3.8 0.3 - - - +
141D PRO* 3.6 3.5 - - - +
142D MET* 2.8 37.6 + - + +
143D SER 3.7 16.4 + - - +
144D ALA* 3.9 18.4 + - + +
145D LYS* 3.6 28.1 - - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 4.2 3.1 + - + +
22D ARG* 1.3 72.7 - - - +
24D TYR* 1.3 62.3 + - - +
25D CYS 3.8 0.5 + - - -
31D PHE* 3.5 3.3 - - - +
32D LEU* 2.9 50.4 + - + +
51D ILE 4.6 0.6 + - - -
53D LEU* 3.8 25.7 - - + +
55D LEU* 4.7 13.2 - - + -
65D ILE* 4.1 24.7 - - + -
106D TYR* 4.0 33.0 - - + +
139D PHE* 4.0 17.5 - - + -
140D LEU 4.0 1.1 - - - -
141D PRO* 4.2 24.2 - - + -
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Residues in contact with TYR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ARG 3.8 1.2 + - - -
23D LEU* 1.3 72.3 - - - +
25D CYS* 1.3 71.5 + - - +
26D LYS* 3.8 9.4 - - + -
29D GLY* 3.5 25.6 - - - -
30D PHE 3.7 3.4 - - - -
31D PHE* 3.8 13.9 - + + -
103D TYR* 5.0 0.9 - + - -
139D PHE* 3.0 6.6 - - - -
140D LEU* 2.7 53.6 + - + +
142D MET* 3.8 14.1 - - - -
164H LYS* 3.0 19.4 + - - -
166H LEU* 2.7 45.0 + - + -
168H ALA* 3.0 48.0 + - + -
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Residues in contact with CYS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU 3.8 0.4 + - - -
24D TYR* 1.3 75.2 - - - +
26D LYS* 1.3 67.7 - - - +
27D ASN* 3.1 26.6 + - - +
29D GLY* 3.0 25.1 + - - -
30D PHE 2.8 18.7 + - - +
118D LEU* 3.8 22.4 - - + -
136D ALA 3.5 25.8 - - - -
138D LEU 3.5 9.0 - - - -
139D PHE* 3.6 19.1 - - + -
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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