Contacts of the strand formed by residues 11 - 21 (chain B) in PDB entry 2LMQ
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 GLU 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR 4.4 18.2 - - - +
11A GLU* 5.6 6.1 - - - -
12A VAL 6.3 0.2 - - - +
9B GLY 4.4 14.6 + - - +
10B TYR* 1.3 82.7 - - - +
12B VAL* 1.3 63.8 + - - +
13B HIS* 4.3 20.5 + - + +
10C TYR 3.1 9.6 + - - +
11C GLU* 3.8 21.2 - - + +
12C VAL* 3.2 30.8 + - - +
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 5.7 2.0 - - + +
12A VAL 2.6 34.1 + - - +
13A HIS* 4.9 1.9 - - - -
14A HIS* 4.6 20.4 - - + +
10B TYR* 2.8 45.7 - - + +
11B GLU* 1.3 74.5 - - - +
13B HIS* 1.3 76.8 + - - +
14B HIS* 4.5 11.0 - - + +
12C VAL* 3.5 15.5 - - + +
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Residues in contact with HIS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 5.9 0.6 - - - -
12A VAL* 3.6 41.8 + - + +
13A HIS 6.2 0.4 - - - -
11B GLU* 4.3 23.8 + - + +
12B VAL* 1.3 93.9 + - - +
14B HIS* 1.3 56.2 + - - +
11C GLU* 5.5 7.4 - - + -
12C VAL 3.1 10.7 + - - +
13C HIS* 2.6 69.9 - + + +
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Residues in contact with HIS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A HIS 5.9 0.2 - - - -
14A HIS* 2.7 42.7 - + + +
12B VAL* 4.2 7.5 - - + +
13B HIS* 1.3 76.0 - - - +
15B GLN* 1.3 97.8 + - - +
16B LYS* 3.5 22.7 - - + +
12C VAL* 5.8 0.4 - - + +
13C HIS* 4.6 2.2 - - - -
14C HIS* 2.5 51.7 + + + +
15C GLN 3.7 1.8 - - - -
16C LYS* 3.3 27.2 - - + +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A HIS* 4.3 1.1 - - - -
15A GLN* 3.1 49.2 + - - +
17A LEU* 3.1 35.8 - - + +
14B HIS* 1.3 110.5 + - - +
16B LYS* 1.3 59.9 + - - +
17B LEU* 3.7 5.7 + - - +
14C HIS 3.9 0.8 + - - -
15C GLN* 4.4 3.5 - - - +
16C LYS 3.6 8.8 + - - +
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A HIS* 5.1 16.7 + - + +
15A GLN 3.2 12.1 + - - +
16A LYS* 4.5 21.5 - - + -
17A LEU* 2.9 36.3 + - - +
14B HIS* 3.5 23.3 - - + +
15B GLN* 1.3 71.3 - - - +
17B LEU* 1.3 59.2 + - - +
18B VAL* 5.4 5.6 - - + -
16C LYS* 4.2 26.9 - - + +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 3.8 31.2 - - + -
19A PHE* 6.3 1.6 - - + -
15B GLN* 3.7 5.6 + - - +
16B LYS* 1.3 73.0 - - - +
18B VAL* 1.3 71.2 + - - +
19B PHE* 5.8 4.0 - - + -
16C LYS* 3.0 19.0 + - - +
17C LEU* 3.7 23.8 - - + -
18C VAL* 2.9 26.8 + - - +
19C PHE* 5.2 11.4 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 6.5 0.4 - - - -
17A LEU 2.8 18.2 + - - +
18A VAL* 3.5 23.0 - - + -
19A PHE* 2.8 33.1 + - - +
16B LYS* 5.2 6.5 - - + -
17B LEU* 1.3 84.0 - - - +
19B PHE* 1.3 59.7 + - - +
20B PHE* 3.5 31.6 - - + -
16C LYS* 5.5 5.2 - - + +
18C VAL* 3.6 20.4 - - + +
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.4 40.2 - + + -
21A ALA* 5.1 1.1 - - + -
28A LYS* 3.6 27.4 - - - -
32A ILE* 6.5 0.2 - - + -
17B LEU* 5.8 5.2 - - + -
18B VAL* 1.3 75.4 - - - +
20B PHE* 1.3 60.4 + - - +
21B ALA* 3.4 26.7 - - + -
18C VAL 2.9 14.3 + - - +
19C PHE* 4.6 17.9 - + + -
20C PHE* 2.7 44.1 + - - +
21C ALA* 5.4 3.6 - - + -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 6.2 1.3 - - + -
19A PHE 2.7 13.6 + - - +
20A PHE* 3.2 11.6 - - + -
21A ALA* 2.9 25.6 + - - +
18B VAL* 3.5 26.2 - - + -
19B PHE* 1.3 81.7 - - - +
21B ALA* 1.3 60.7 + - - +
22B GLU* 6.1 0.2 - - - -
18C VAL* 4.6 11.2 - - + -
20C PHE* 2.9 59.0 - + + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.3 4.7 - - + +
28A LYS* 3.5 29.8 - - + +
19B PHE* 3.4 24.9 - - + -
20B PHE* 1.3 76.1 - - - +
22B GLU* 1.3 63.1 + - - +
23B ASP* 3.6 6.1 - - - +
20C PHE* 2.9 12.6 + - - +
21C ALA* 3.3 4.9 - - + -
22C GLU* 3.0 27.7 + - - +
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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