Contacts of the strand formed by residues 11 - 18 (chain G) in PDB entry 1L0N
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 ARG 11 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ARG 3.8 2.2 - - - -
245A GLU* 2.6 41.7 + - - +
246A ASP* 4.1 3.6 - - + +
247A GLY* 3.7 12.6 - - - +
248A LEU* 5.3 1.0 - - - +
237D TYR* 3.9 6.9 - - - -
52F GLU* 3.4 33.1 + - - +
56F ASP* 3.5 18.6 + - - +
59F VAL* 4.9 3.6 - - - +
9G ARG* 3.6 32.6 - - + +
10G VAL* 1.3 82.7 - - - +
12G HIS* 1.3 99.4 + - + +
13G VAL* 3.6 10.6 - - - +
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Residues in contact with HIS 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A HIS* 4.3 13.5 + - - +
244A ARG 3.0 14.1 + - - -
245A GLU* 3.9 14.4 - - - +
237D TYR* 3.1 21.5 - + + -
238D ARG 3.2 35.2 + - - +
239D PRO* 4.0 4.7 - - + -
240D PRO* 3.4 37.4 - - + +
52F GLU* 5.6 0.8 - - - +
56F ASP* 3.4 26.6 + - + -
11G ARG* 1.3 117.5 + - + +
13G VAL* 1.3 56.5 + - - +
14G ILE* 5.3 0.7 - - - -
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Residues in contact with VAL 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A CYS 3.6 1.0 - - - +
243A HIS* 4.6 0.8 - - - -
244A ARG* 3.2 28.8 + - + +
235D LEU* 4.5 3.1 - - + -
236D ALA 3.4 10.1 - - - +
237D TYR* 4.3 4.0 - - + -
59F VAL* 4.7 7.9 - - + -
60F PHE* 4.2 24.9 - - + -
63F LYS* 3.8 31.0 - - + -
10G VAL* 3.9 23.1 - - + -
11G ARG 3.6 10.8 - - - +
12G HIS* 1.3 82.3 - - - +
14G ILE* 1.3 71.6 + - - +
15G THR* 4.5 3.0 + - - +
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Residues in contact with ILE 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ILE* 3.9 14.8 - - + -
242A CYS 3.2 11.4 - - - +
243A HIS* 4.1 23.8 - - + +
234D LYS 4.4 0.2 - - - -
235D LEU* 3.5 6.4 - - - +
236D ALA* 2.8 31.1 + - + +
238D ARG* 3.7 26.9 - - + -
5E ILE* 3.6 30.3 - - + -
13G VAL* 1.3 76.6 - - - +
15G THR* 1.3 69.3 + - - +
16G TYR* 3.6 42.0 - - + +
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Residues in contact with THR 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLN* 3.6 4.3 - - - +
242A CYS* 2.9 42.2 + - - +
233D ARG* 4.1 19.3 - - + +
234D LYS 3.3 9.9 - - - +
235D LEU* 3.1 18.8 - - + +
63F LYS* 4.4 10.2 + - - -
13G VAL* 4.5 2.8 + - - +
14G ILE* 1.3 78.1 + - - +
16G TYR* 1.3 70.6 + - - +
17G SER* 3.7 7.5 + - - +
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Residues in contact with TYR 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLN 3.5 4.9 - - - +
241A ILE* 3.9 22.0 - - + -
233D ARG* 3.5 4.7 - - - -
234D LYS* 3.0 46.0 + - + +
235D LEU 5.1 0.9 - - - -
236D ALA* 4.2 17.0 - - + -
5E ILE* 3.4 14.3 - - + +
6E LYS* 2.9 44.2 + - - -
7E VAL* 3.8 13.7 - - + -
8E PRO* 3.6 37.7 - - + -
10E PHE* 4.4 11.8 - - + -
14G ILE* 3.6 27.3 - - + +
15G THR* 1.3 75.4 - - - +
17G SER* 1.3 62.0 + - - +
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Residues in contact with SER 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN* 4.6 2.4 + - - -
239A SER* 3.1 20.1 - - - -
240A GLN* 2.8 29.5 + - - +
434A TYR* 5.1 3.4 - - - -
229D VAL* 3.6 34.3 + - - +
230D LEU* 5.5 1.4 - - - +
233D ARG* 4.6 3.7 - - - +
10E PHE* 4.5 7.9 - - - -
15G THR* 4.5 10.7 + - - +
16G TYR* 1.3 77.4 + - - +
18G LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN* 4.4 5.6 - - - +
237A THR* 3.5 31.4 - - + -
238A GLY 3.8 4.0 - - - +
239A SER* 4.0 7.6 - - - -
434A TYR* 5.4 1.8 - - - -
229D VAL* 3.9 17.6 + - - +
232D SER 5.1 0.8 + - - -
10E PHE* 3.6 42.5 - - + -
14E ARG* 4.1 11.4 - - + +
17G SER* 1.3 77.5 - - - +
19G SER* 1.3 75.2 + - - +
20G PRO 3.6 1.2 - - - -
22G GLU* 3.7 23.3 - - + +
23G GLN* 3.0 33.0 + - + +
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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