Contacts of the strand formed by residues 24 - 29 (chain A) 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 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.8 7.4 - - + -
17A SER 3.8 3.6 - - - +
18A GLN* 3.7 29.8 + - + +
22A GLY 3.2 11.5 + - - -
23A LEU* 1.3 78.8 - - - +
25A VAL* 1.3 59.7 + - - +
26A ALA 4.1 0.7 - - - -
193A PRO 3.6 22.8 + - - -
195A MET 3.5 4.0 + - - -
196A VAL* 3.3 29.6 - - + +
197A LEU 2.9 25.3 + - - +
383A LEU* 2.7 53.9 + - + +
384A LEU* 4.0 12.3 - - - +
387A GLY* 4.5 9.2 + - - -
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Residues in contact with VAL 25 (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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16A VAL* 5.1 0.2 - - - -
17A SER* 2.8 43.2 + - - +
19A LEU* 4.4 8.3 - - + -
23A LEU* 4.4 3.8 - - + +
24A ARG* 1.3 75.3 - - - +
26A ALA* 1.3 60.9 + - - +
197A LEU* 3.4 12.6 - - + +
205A HIS* 3.3 10.3 - - + -
208A LEU* 3.7 46.2 - - + +
209A LEU* 3.7 26.2 - - + +
212A ALA* 4.1 15.9 - - + -
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Residues in contact with ALA 26 (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 THR* 4.6 1.8 - - + -
15A GLN 3.2 12.1 - - - +
16A VAL* 4.1 19.3 - - + -
24A ARG 4.1 0.6 - - - -
25A VAL* 1.3 74.4 - - - +
27A SER* 1.3 62.4 + - - +
196A VAL* 5.0 2.6 - - + +
197A LEU 3.1 7.4 + - - +
198A ALA* 3.4 6.9 - - - +
199A ALA 3.1 22.7 + - - +
205A HIS* 4.2 0.7 - - - -
208A LEU* 3.6 4.5 - - - +
379A ILE* 3.7 23.0 - - + +
383A LEU* 4.2 12.3 - - + -
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Residues in contact with SER 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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13A GLU 4.4 0.5 - - - +
14A THR* 3.5 5.6 - - - +
15A GLN* 2.9 32.4 + - - +
26A ALA* 1.3 77.0 - - - +
28A GLU* 1.3 62.0 + - - +
29A GLN* 4.2 3.5 + - - +
199A ALA 3.4 11.2 - - - -
203A LEU* 4.7 10.3 - - - -
205A HIS* 2.8 38.9 + - - +
208A LEU* 3.7 19.7 - - - -
379A ILE* 4.3 1.1 - - - -
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Residues in contact with GLU 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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11A VAL* 4.0 22.8 - - - +
12A PRO* 3.9 21.7 - - + +
13A GLU 4.9 1.6 - - - -
14A THR* 4.1 11.6 + - - +
27A SER* 1.3 73.7 - - - +
29A GLN* 1.3 69.7 + - - +
30A SER* 3.4 6.8 + - - -
199A ALA 3.4 6.7 + - - -
200A ALA* 3.6 3.6 - - + +
201A GLY 3.3 20.6 + - - -
203A LEU* 5.4 0.4 - - - -
375A VAL* 3.6 20.1 - - + +
379A ILE* 3.9 15.9 - - + +
389A ARG* 3.0 26.2 + - - -
392A LEU* 5.7 0.2 - - - +
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Residues in contact with GLN 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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12A PRO* 3.6 21.0 - - + +
13A GLU 5.4 1.0 + - - -
27A SER* 4.0 4.9 + - - +
28A GLU* 1.3 76.3 - - - +
30A SER* 1.3 71.9 + - - +
201A GLY 3.4 6.5 - - - +
202A GLY* 5.6 1.4 - - - -
203A LEU* 3.2 30.4 + - - +
204A GLU* 3.9 24.3 + - - +
205A HIS 5.0 3.0 + - - +
17B VAL 4.4 9.0 + - - +
18B PRO* 3.4 37.3 - - + +
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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