Contacts of the strand formed by residues 239 - 245 (chain A) in PDB entry 3H1J
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 SER 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A THR* 2.8 31.6 + - - +
159A GLN* 3.3 5.1 + - - -
237A THR 2.7 16.3 + - - -
238A GLY* 1.3 75.8 - - - -
240A GLU* 1.3 63.3 + - - +
420A PRO 3.1 5.8 + - - +
421A ALA* 3.2 4.0 - - - -
422A LEU 2.8 22.2 + - - -
434A TYR* 3.7 8.5 - - - -
17G SER 3.2 16.4 - - - -
18G LEU* 3.3 20.2 - - - +
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Residues in contact with GLU 240 (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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156A THR* 3.9 6.4 + - - -
239A SER* 1.3 76.4 - - - +
241A ILE* 1.3 62.5 + - - +
242A ARG* 2.8 48.8 + - - +
422A LEU* 3.1 28.6 - - + +
434A TYR* 3.2 36.0 + - + +
229D VAL* 5.7 0.7 - - - +
15G THR* 4.9 3.3 + - - +
16G TYR* 3.4 4.9 - - - +
17G SER* 2.9 53.6 + - - +
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Residues in contact with ILE 241 (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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152A TYR* 3.8 44.6 - - + +
155A ALA* 5.2 1.3 - - + -
156A THR* 3.5 23.1 - - + -
240A GLU* 1.3 74.7 - - - +
242A ARG* 1.3 64.8 + - - +
243A ALA 4.6 0.2 - - - +
422A LEU 2.9 13.7 + - - +
423A ALA* 3.4 8.3 - - + -
424A ALA 3.1 22.2 + - - +
5E VAL* 4.2 8.3 - - + -
7E VAL* 4.9 5.6 - - + -
14G ILE* 3.8 19.1 - - + -
15G THR 3.3 4.7 - - - +
16G TYR* 3.7 27.6 - - + -
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Residues in contact with ARG 242 (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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240A GLU* 2.8 45.1 + - + +
241A ILE* 1.3 73.8 - - - +
243A ALA* 1.3 59.8 + - - +
244A ARG* 3.5 2.1 + - + +
422A LEU* 3.8 4.0 - - + +
424A ALA* 3.7 9.9 - - + +
428A ILE* 3.8 19.8 + - + +
431A LEU* 3.3 22.9 + - - +
432A LEU* 3.2 35.3 - - - +
433A ASP* 3.1 28.5 - - - +
434A TYR 3.6 0.2 - - - +
437A ILE* 3.8 12.9 - - - +
13G ILE 3.3 5.2 - - - +
14G ILE* 3.1 6.2 - - - -
15G THR* 2.9 45.7 + - - +
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Residues in contact with ALA 243 (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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152A TYR* 3.5 34.1 - - + +
241A ILE 3.8 1.8 + - - -
242A ARG* 1.3 71.0 - - - +
244A ARG* 1.3 58.6 + - - +
245A ASP* 3.9 0.5 + - - +
424A ALA 2.9 12.6 + - - +
425A VAL* 3.2 13.2 - - + +
426A GLY 3.2 20.6 + - - -
428A ILE* 4.3 0.8 - - - +
14G ILE* 4.0 23.6 - - + -
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Residues in contact with ARG 244 (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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242A ARG* 3.5 1.8 + - + +
243A ALA* 1.3 73.9 - - - +
245A ASP* 1.3 57.4 + - - +
246A ASP* 2.7 36.7 + - - +
426A GLY 3.4 12.1 - - - +
428A ILE* 4.0 18.8 - - + -
429A GLU* 3.0 50.2 + - - +
432A LEU* 6.0 1.2 - - - +
215C ASP 5.3 3.2 + - - -
216C SER 5.3 5.5 + - - -
63F LYS* 6.0 0.8 - - - +
8G ALA 3.1 9.3 + - - -
10G VAL* 3.5 35.5 - - + +
11G ARG 3.6 0.5 - - - -
12G HIS* 2.8 31.0 + - - -
13G ILE* 3.1 23.9 + - + +
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Residues in contact with ASP 245 (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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243A ALA 3.9 1.5 + - - +
244A ARG* 1.3 75.6 - - - +
246A ASP* 1.3 53.5 + - - +
247A ALA* 2.8 18.6 + - - +
248A LEU* 3.1 36.8 + - + +
425A VAL* 6.1 0.4 - - + -
426A GLY* 2.8 24.7 + - - +
427A PRO 3.4 0.3 - - - -
10G VAL 3.9 2.7 - - - -
11G ARG* 2.5 47.6 + - - +
12G HIS* 3.7 16.2 + - + +
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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