Contacts of the strand formed by residues 26 - 34 (chain A) in PDB entry 4LL1
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LYS* 5.3 1.0 + - - -
21A TYR* 3.7 16.2 - - - -
24A GLY 4.1 1.0 + - - -
25A GLU* 1.3 82.8 + - - +
27A VAL* 1.3 65.2 + - - +
28A ALA* 4.0 13.6 + - + +
102A GLY* 4.0 23.0 + - - -
103A PHE* 3.7 11.9 - - - +
104A GLU* 4.0 28.3 + - + +
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Residues in contact with VAL 27 (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 PHE* 3.7 34.1 - - + -
21A TYR* 3.9 33.9 - - + -
26A LYS* 1.3 76.3 - - - +
28A ALA* 1.3 61.1 + - - +
101A PHE* 4.6 1.1 - - + -
102A GLY* 3.2 2.3 - - - -
103A PHE* 2.8 69.2 + - + -
105A LEU* 4.0 20.9 - - + -
143A PHE* 4.4 7.2 - - + -
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Residues in contact with ALA 28 (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 PHE* 3.8 6.5 - - - +
15A ASN* 3.1 37.9 + - - +
21A TYR* 4.6 4.8 + - - -
26A LYS* 4.0 14.6 + - + +
27A VAL* 1.3 76.3 - - - +
29A GLY* 1.3 58.9 + - - +
101A PHE* 3.4 17.0 - - - +
102A GLY* 4.1 3.8 - - - -
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Residues in contact with GLY 29 (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 3.5 11.4 - - - -
14A PHE* 4.1 0.2 - - - -
15A ASN* 3.8 12.9 + - - +
28A ALA* 1.3 76.4 - - - +
30A ARG* 1.3 69.5 + - - +
100A LYS* 3.6 4.3 - - - +
101A PHE* 3.0 41.9 + - - +
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Residues in contact with ARG 30 (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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11A GLU 3.8 0.3 - - - +
12A VAL* 3.7 1.9 - - - -
13A VAL* 2.9 65.8 + - - +
14A PHE 4.4 0.4 + - - -
15A ASN* 2.7 36.5 + - - +
29A GLY* 1.3 77.5 - - - +
31A VAL* 1.3 61.8 + - - +
32A ILE* 3.8 32.4 + - + +
98A GLU* 4.0 30.4 + - + -
99A TYR 3.2 14.4 - - - +
100A LYS* 4.4 11.0 - - + +
101A PHE* 3.4 8.5 - - - -
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Residues in contact with VAL 31 (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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10A PHE* 3.6 31.6 - - + -
11A GLU 3.4 9.2 - - - +
12A VAL* 4.7 5.2 - - + -
30A ARG* 1.3 74.2 - - - +
32A ILE* 1.3 61.7 + - - +
33A VAL* 4.1 2.5 - - + -
44A VAL* 4.0 8.7 - - + -
46A ILE* 3.9 16.8 - - + -
76A LEU* 3.6 24.0 - - + -
97A TYR 3.5 3.3 - - - +
98A GLU* 3.5 0.3 - - - -
99A TYR* 2.8 49.0 + - + -
101A PHE* 4.0 8.0 - - + -
127A ALA* 3.9 14.8 - - + -
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Residues in contact with ILE 32 (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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9A SER* 3.7 4.5 + - - +
10A PHE* 3.4 7.3 + - - -
11A GLU* 3.0 33.3 + - + +
13A VAL* 3.9 21.1 - - + -
30A ARG* 3.8 42.8 - - + +
31A VAL* 1.3 77.8 - - - +
33A VAL* 1.3 62.9 + - - +
34A GLU* 4.1 20.2 - - + +
96A LYS* 4.7 10.1 - - + -
97A TYR 3.4 6.3 - - - +
98A GLU* 4.3 23.3 - - + +
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Residues in contact with VAL 33 (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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7A ILE* 4.5 6.3 - - + -
9A SER 3.6 9.4 - - - +
10A PHE* 3.7 28.9 - - + -
31A VAL* 4.6 1.3 - - + -
32A ILE* 1.3 76.7 - - - +
34A GLU* 1.3 73.5 + - - +
44A VAL* 4.3 4.9 - - + -
91A MET* 3.7 37.9 - - + -
97A TYR* 2.8 42.2 + - - +
99A TYR* 4.0 17.9 - - + -
129A LEU* 4.5 15.7 - - + -
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Residues in contact with GLU 34 (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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7A ILE* 3.8 4.9 - - - +
8A LYS* 3.3 51.9 + - - +
9A SER* 3.2 30.6 + - - +
32A ILE* 4.1 10.9 - - + +
33A VAL* 1.3 83.7 - - - +
35A VAL* 1.3 63.0 + - - +
95A ASN 3.6 18.6 - - - +
96A LYS* 3.4 33.5 - - - +
97A TYR* 5.0 1.6 - - - -
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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