Contacts of the strand formed by residues 13 - 18 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A MET 3.0 11.2 + - - +
12A PRO* 1.3 74.8 - - - +
14A ALA* 1.3 69.8 + - - +
36A LEU* 3.9 28.3 - - + -
37A LEU* 3.6 1.2 - - - -
38A ALA* 3.1 49.9 + - + +
39A ASN* 4.1 2.2 - - - +
41A VAL* 3.7 3.3 - - - +
154A ILE 3.5 9.0 - - - +
155A ILE* 4.0 8.7 - - + -
55B LEU* 4.0 21.8 - - + -
123B VAL* 4.0 21.3 - - + -
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Residues in contact with ALA 14 (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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13A VAL* 1.3 80.6 - - - +
15A HIS* 1.3 61.7 + - - +
16A VAL* 4.0 1.6 - - + -
36A LEU* 3.1 10.1 - - - +
37A LEU* 4.3 5.6 - - + -
41A VAL* 3.8 23.6 - - + -
48A LEU* 4.0 15.7 - - + -
59A TYR* 3.7 2.9 + - - -
153A GLY* 2.8 4.9 - - - -
154A ILE* 2.7 47.8 + - + +
123B VAL* 5.5 0.2 - - - +
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Residues in contact with HIS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 1.3 73.7 - - - +
16A VAL* 1.3 58.4 + - - +
17A VAL* 4.2 12.3 - - + +
34A ASN 3.6 20.2 - - - +
35A ALA* 3.2 7.7 - - - +
36A LEU* 2.7 38.2 + - + +
59A TYR* 2.8 24.7 + + - +
148A GLY* 6.1 0.4 - - - -
151A TYR* 3.6 41.7 - + + +
152A PHE 3.6 3.7 + - - -
93B LEU 5.0 1.6 + - - -
94B LEU* 4.8 0.4 - - - +
122B GLY* 4.3 0.9 - - - -
123B VAL* 3.5 19.7 + - + +
124B PHE* 3.4 31.6 - + - -
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Residues in contact with VAL 16 (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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14A ALA* 5.1 0.7 - - + -
15A HIS* 1.3 77.2 - - - +
17A VAL* 1.3 60.8 - - - +
28A TRP* 3.7 26.2 - - + -
29A LEU 3.3 16.8 - - - +
30A ASN* 4.0 12.1 - - + +
36A LEU 4.3 6.3 - - - +
37A LEU* 4.9 4.0 - - + -
43A LEU* 4.0 20.2 - - + -
48A LEU* 4.2 19.3 - - + -
151A TYR* 3.5 4.3 - - - +
152A PHE* 2.9 59.0 + - + +
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Residues in contact with VAL 17 (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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15A HIS* 4.2 23.6 - - + +
16A VAL* 1.3 77.1 - - - +
18A ALA* 1.3 69.2 + - - +
20A PRO* 6.3 0.2 - - + -
28A TRP* 3.3 7.0 - - - -
29A LEU* 2.7 43.2 + - + +
32A ARG* 4.4 24.7 - - + -
34A ASN 5.0 3.4 - - - +
35A ALA* 4.7 7.4 - - + +
148A GLY* 5.6 9.2 - - - +
150A VAL 3.7 12.6 - - - +
151A TYR* 4.7 1.1 - - + -
73R SER* 4.7 5.8 - - - +
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Residues in contact with ALA 18 (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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17A VAL* 1.3 84.0 - - - +
19A ASN* 1.3 60.1 + - - +
20A PRO* 3.1 16.5 - - - +
26A LEU* 3.5 27.4 - - + -
27A GLN 3.5 4.9 - - - -
28A TRP* 3.9 3.5 - - - -
29A LEU* 4.6 0.4 - - - -
144A PHE* 3.7 19.7 - - + -
150A VAL* 3.4 27.2 + - + -
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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