Contacts of the strand formed by residues 22 - 28 (chain A) in PDB entry 1LCG
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 HIS 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLN* 5.3 11.1 + - - -
19A GLY* 6.0 1.3 - - - -
20A SER 4.1 15.6 + - - -
21A LEU* 1.3 73.3 - - - +
23A ARG* 1.3 54.6 + - - +
156A GLU* 2.6 43.1 + - - +
158A LEU* 2.9 44.8 - - + +
209A LEU 3.9 10.9 + - - -
210A VAL* 4.8 7.5 - - + -
211A ASP* 5.1 6.9 + - + +
232A ILE* 3.4 8.6 - - - +
233A PHE 3.0 29.3 + - - +
234A GLY 6.0 0.2 - - - -
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Residues in contact with ARG 23 (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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21A LEU* 2.9 49.2 + - + +
22A HIS* 1.3 79.1 - - - +
24A VAL* 1.4 57.9 + - - +
25A PRO* 3.3 8.7 - - - +
156A GLU* 3.4 18.8 + - - +
230A GLU* 2.8 34.5 - - + +
231A LEU 3.5 2.5 - - - -
232A ILE* 4.4 12.6 - - + +
237A ASP* 3.0 19.9 + - - -
240A HIS* 5.3 10.4 - - - -
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Residues in contact with VAL 24 (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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23A ARG* 1.4 70.3 - - - +
25A PRO* 1.3 70.7 - - + +
26A LEU* 3.1 7.1 - - + +
80A GLY* 5.9 0.2 - - - -
81A THR 5.0 7.0 - - - +
95A PHE* 4.4 14.1 - - + -
155A VAL* 3.6 22.2 - - + -
156A GLU* 2.9 33.6 - - + +
230A GLU* 3.0 5.4 - - - -
231A LEU* 2.8 62.4 + - + +
233A PHE* 4.2 5.2 - - + -
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Residues in contact with PRO 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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23A ARG 3.3 6.7 - - - +
24A VAL* 1.3 89.8 - - + +
26A LEU* 1.4 63.1 + - - +
27A ARG* 5.6 3.0 - - + +
80A GLY* 3.9 15.1 - - - -
81A THR* 4.8 2.6 + - - +
227A ALA 5.9 0.7 - - - +
229A SER 4.2 1.1 - - - +
230A GLU* 2.8 29.8 - - - +
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Residues in contact with LEU 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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24A VAL* 3.1 28.9 - - + +
25A PRO* 1.4 76.1 - - - +
27A ARG* 1.3 56.9 + - - +
78A TYR* 4.3 17.0 - - + +
79A PHE* 3.1 37.5 - - - +
80A GLY* 3.3 9.4 - - - +
95A PHE* 3.8 20.2 - - + +
217A VAL* 6.1 0.7 - - + -
227A ALA 2.5 28.1 - - - +
228A GLY* 3.2 0.4 - - - -
229A SER* 2.8 40.8 + - - +
230A GLU 3.8 0.4 - - - -
231A LEU* 3.5 17.5 - - + +
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Residues in contact with ARG 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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25A PRO* 5.6 2.7 - - + +
26A LEU* 1.3 77.8 - - - +
28A ARG* 1.3 60.8 + - - +
29A HIS* 3.0 38.5 + - + -
78A TYR* 3.3 4.5 - - - -
79A PHE 2.8 31.6 + - - +
227A ALA* 3.9 10.9 - - + +
228A GLY* 4.5 2.0 - - - -
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Residues in contact with ARG 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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27A ARG* 1.3 73.7 + - - +
29A HIS* 1.4 69.6 + - - +
34A LYS* 4.8 9.1 - - - +
77A GLU* 3.1 45.4 + - - +
78A TYR* 3.4 29.4 + - + -
220A SER 5.4 1.6 + - - -
221A SER 5.3 6.1 + - - -
227A ALA* 4.9 4.5 - - + +
228A GLY* 4.2 11.5 - - - +
341A LEU* 4.5 8.1 - - - +
342A LEU* 4.5 18.6 + - - +
345A VAL* 4.8 25.8 - - + +
376A ARG* 3.4 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