Contacts of the strand formed by residues 13 - 18 (chain C) in PDB entry 3ALQ
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 13 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.7 24.7 - - + -
123A VAL* 4.0 8.5 - - + -
11C MET 3.9 4.9 - - - +
12C PRO* 1.3 75.5 - - - +
14C ALA* 1.3 76.5 + - - +
36C LEU* 3.8 31.0 - - + -
37C LEU* 3.7 0.3 - - - -
38C ALA* 3.0 52.4 + - + +
39C ASN* 4.6 1.6 - - - +
41C VAL* 4.0 6.2 - - - +
154C ILE 3.4 9.4 - - - +
155C ILE* 3.7 23.6 - - + -
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Residues in contact with ALA 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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13C VAL* 1.3 81.2 - - - +
15C HIS* 1.3 61.5 + - - +
16C VAL* 4.0 1.3 - - + +
36C LEU* 3.1 12.8 - - - +
37C LEU* 4.1 6.5 - - + -
41C VAL* 3.8 23.6 - - + -
48C LEU* 4.1 13.9 - - + -
59C TYR* 3.9 2.4 + - - -
153C GLY* 2.9 4.0 - - - -
154C ILE* 2.8 47.7 + - + +
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Residues in contact with HIS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU 4.8 2.4 + - - -
122A GLY* 4.5 1.1 - - - -
123A VAL* 3.7 13.8 + - + +
124A PHE* 3.8 27.5 - + - -
14C ALA* 1.3 72.0 - - - +
16C VAL* 1.3 58.1 + - - +
17C VAL* 4.2 10.9 - - + +
34C ASN 3.6 20.4 - - - +
35C ALA* 3.4 6.3 - - - +
36C LEU* 2.7 39.6 + - + +
59C TYR* 2.6 31.4 + + - +
148C GLY* 6.2 0.4 - - - -
151C TYR* 3.3 46.7 - + + +
152C PHE 3.3 3.7 + - - -
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C HIS* 1.3 76.1 - - - +
17C VAL* 1.3 60.3 + - - +
28C TRP* 3.6 24.2 - - + -
29C LEU 3.0 21.3 - - - +
30C ASN* 3.9 13.0 - - + +
36C LEU 4.2 5.8 - - - +
37C LEU* 4.9 2.7 - - + -
43C LEU* 3.9 21.1 - - + -
48C LEU* 4.4 18.6 - - + -
151C TYR* 3.3 6.6 - - - +
152C PHE* 2.8 59.7 + - + +
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C HIS* 4.2 24.0 - - + +
16C VAL* 1.3 80.6 - - - +
18C ALA* 1.3 69.7 + - - +
20C PRO* 6.2 0.2 - - + -
28C TRP* 3.3 8.8 - - - -
29C LEU* 2.7 41.1 + - + +
32C ARG* 4.5 24.9 - - + -
34C ASN 5.2 1.8 - - - +
35C ALA* 4.6 8.1 - - + -
148C GLY* 6.0 6.7 - - - +
150C VAL 3.6 12.8 - - - +
151C TYR* 4.5 1.1 - - + -
73T SER* 5.1 3.8 - - - +
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Residues in contact with ALA 18 (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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17C VAL* 1.3 83.5 - - - +
19C ASN* 1.3 59.8 + - - +
20C PRO* 3.0 17.5 - - - +
26C LEU* 3.8 10.3 - - + -
27C GLN 3.7 5.2 - - - +
28C TRP* 3.9 1.4 - - - -
144C PHE* 3.7 29.3 - - + +
150C VAL* 3.3 35.1 + - + +
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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