Contacts of the strand formed by residues 21 - 25 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C HIS 3.3 28.9 + - - +
17C PHE* 4.6 10.1 - - - +
19C ASP* 3.5 14.9 + - - +
20C PRO* 1.3 79.8 + - - +
22C ARG* 1.3 69.6 + - - +
23C LEU* 5.5 4.3 - - + -
51C ILE 3.5 0.2 - - - +
52C LYS* 4.8 0.2 - - - -
53C LEU* 2.7 44.3 + - + +
55C LEU* 5.7 14.1 - - + +
141C PRO* 4.0 24.9 - - + -
142C MET 3.2 15.7 - - - +
143C SER* 5.3 4.6 - - - +
144C ALA* 4.3 4.9 - - - +
283G ASP 5.6 4.7 - - - -
285G GLN* 5.3 7.0 - - - +
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LYS* 1.3 77.2 - - - +
23C LEU* 1.3 62.6 + - - +
24C TYR 3.8 0.4 + - - -
31C PHE* 4.0 29.6 - - + -
46C LYS* 3.4 31.7 + - - +
48C ASP 4.6 2.4 + - - -
51C ILE* 3.5 40.4 - - + +
52C LYS* 4.8 6.9 - - - +
140C LEU 3.8 0.3 - - - +
141C PRO* 3.6 3.5 - - - +
142C MET* 2.8 37.6 + - + +
143C SER 3.6 16.6 + - - +
144C ALA* 3.8 18.2 + - + +
145C LYS* 3.6 28.3 - - - +
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LYS* 4.2 4.9 + - + +
22C ARG* 1.3 75.9 - - - +
24C TYR* 1.3 62.2 + - - +
25C CYS 3.8 0.5 + - - -
31C PHE* 3.5 3.1 - - - +
32C LEU* 2.9 50.1 + - + +
51C ILE 4.6 0.6 + - - -
53C LEU* 3.8 26.6 - - + +
55C LEU* 4.8 11.2 - - + -
65C ILE* 4.2 24.2 - - + -
106C TYR* 4.1 31.0 - - + +
139C PHE* 3.9 18.0 - - + -
140C LEU 4.0 1.1 - - - -
141C PRO* 4.1 21.3 - - + -
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG 3.8 1.2 + - - -
23C LEU* 1.3 72.0 - - - +
25C CYS* 1.3 70.2 + - - +
26C LYS* 3.9 9.4 - - + -
29C GLY* 3.5 26.2 - - - -
30C PHE 3.7 3.6 - - - -
31C PHE* 3.7 28.5 - + + -
103C TYR* 5.0 0.9 - + - -
139C PHE* 3.0 6.4 - - - -
140C LEU* 2.7 53.5 + - + +
142C MET* 3.8 7.2 - - - -
164G LYS* 3.0 19.2 + - - -
166G LEU* 2.7 37.5 + - + -
168G ALA* 3.0 48.6 + - + -
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Residues in contact with CYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU 3.8 0.4 + - - -
24C TYR* 1.3 74.1 - - - +
26C LYS* 1.3 67.3 - - - +
27C ASN* 3.1 26.9 + - - +
29C GLY* 3.0 25.1 + - - -
30C PHE 2.8 18.7 + - - +
118C LEU* 4.0 23.1 - - + -
136C ALA 3.5 25.4 - - - -
138C LEU 3.5 8.7 - - - -
139C PHE* 3.7 19.3 - - + -
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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