Contacts of the strand formed by residues 9 - 14 (chain C) in PDB entry 2YVL
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 TYR 9 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C GLY 4.6 1.6 - - - -
8C GLU* 1.3 86.6 - - - +
10C VAL* 1.3 59.2 + - - +
20C LEU* 4.1 25.1 - - + -
21C ARG* 3.6 3.1 - - - -
22C LYS* 3.7 51.5 + - + +
57C ARG* 4.5 4.5 - - - +
58C PRO* 3.4 18.7 - - + +
135C LYS* 3.8 41.4 + - + +
136C PHE* 3.8 29.6 - + + -
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Residues in contact with VAL 10 (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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4C PHE* 3.5 27.4 - - + -
8C GLU 3.8 0.2 + - - -
9C TYR* 1.3 75.2 - - - +
11C LEU* 1.3 58.2 + - - +
12C ILE* 3.7 24.9 - - + -
19C PHE 3.6 0.7 - - - +
20C LEU* 3.4 10.1 - - - +
21C ARG* 2.9 42.4 + - + +
23C LEU* 3.4 29.8 - - + -
41C VAL* 5.6 0.9 - - + -
55C VAL* 3.9 18.6 - - + -
56C TYR 3.0 20.4 - - - +
58C PRO* 4.3 0.2 - - - -
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Residues in contact with LEU 11 (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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10C VAL* 1.3 72.5 - - - +
12C ILE* 1.3 67.6 + - - +
18C LYS* 4.3 11.7 - - + -
19C PHE 3.4 6.7 - - - +
20C LEU* 4.4 7.2 - - + -
54C GLU 3.7 0.5 - - - +
55C VAL* 3.4 2.4 - - - -
56C TYR* 2.6 48.0 + - + +
57C ARG 4.3 1.6 - - - +
58C PRO* 4.0 19.1 - - + +
62C GLU* 3.2 49.6 - - + +
66C LEU* 3.7 23.6 - - + -
209D ASN* 3.2 23.1 - - - +
244D ARG* 4.9 1.3 - - - +
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Residues in contact with ILE 12 (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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10C VAL* 3.7 26.0 - - + -
11C LEU* 1.3 78.3 - - - +
13C ARG* 1.3 65.0 + - - +
18C LYS* 3.4 3.9 - - - +
19C PHE* 2.7 48.6 + - + +
21C ARG* 3.9 22.2 - - + -
29C LEU* 3.9 19.1 - - + -
36C LEU* 3.9 25.1 - - + -
38C PHE* 4.1 6.5 - - + -
53C PHE* 3.5 32.8 - - + -
54C GLU 3.3 8.3 - - - +
55C VAL* 4.1 6.1 - - + -
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Residues in contact with ARG 13 (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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11C LEU* 4.1 1.2 + - - +
12C ILE* 1.3 74.9 - - - +
14C PHE* 1.3 59.5 + - - +
15C GLY 2.7 25.9 + - - +
16C GLU* 3.7 22.2 + - - +
17C LYS 3.2 17.5 - - - +
18C LYS* 4.3 12.1 - - + +
52C GLY 3.9 1.9 - - - +
53C PHE* 3.6 3.8 - - - -
54C GLU* 2.8 51.7 + - + +
56C TYR* 4.9 1.1 - - + -
222C THR* 4.4 11.1 + - - -
209D ASN* 2.9 55.9 + - + +
210D LEU 2.8 31.9 + - - +
211D GLU* 4.4 1.4 - - - +
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Residues in contact with PHE 14 (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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12C ILE 4.1 0.6 - - - -
13C ARG* 1.3 74.0 - - - +
15C GLY* 1.3 66.6 + - - +
17C LYS* 2.8 46.2 + - - +
19C PHE* 4.3 7.8 - - + -
31C VAL* 3.5 25.6 - - + -
32C LYS* 5.3 9.9 - - + -
34C SER* 3.5 22.7 - - - -
51C ASN 3.8 10.1 - - - -
52C GLY* 3.3 27.1 - - - -
53C PHE* 3.5 45.1 - + + -
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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