Contacts of the strand formed by residues 35 - 40 (chain A) in PDB entry 3EDY
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 TRP 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.8 29.7 - - + +
32A PRO* 3.3 32.3 + - + +
33A PRO 3.2 15.3 + - - -
34A GLY* 1.3 83.8 + - - +
36A VAL* 1.3 65.8 + - - +
141A TYR* 3.8 7.2 - - + -
142A VAL 3.3 19.7 - - - -
143A GLY* 3.5 7.2 - - - -
148A THR* 3.4 31.0 - - + -
150A VAL* 3.7 19.5 - - + -
176A PHE* 3.5 22.6 - + - +
177A PRO* 3.6 46.4 + - + -
179A THR* 3.6 24.7 + - + +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.8 1.6 - - - -
34A GLY 5.2 3.6 - - - +
35A TRP* 1.3 79.9 - - - +
37A SER* 1.3 75.1 + - - +
38A LEU* 3.6 11.6 + - + +
141A TYR* 3.2 9.6 - - - -
142A VAL* 2.8 45.6 + - + +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.5 10.7 - - - +
36A VAL* 1.3 82.0 - - - +
38A LEU* 1.3 62.9 + - - +
39A GLY 3.6 1.4 + - - -
139A HIS* 4.0 16.3 + - - +
140A HIS 4.0 1.9 + - - -
141A TYR* 3.4 31.7 + - - -
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Residues in contact with LEU 38 (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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36A VAL* 4.0 14.1 - - + +
37A SER* 1.3 76.7 - - - +
39A GLY* 1.3 56.2 + - - +
140A HIS* 2.7 26.4 + - + +
141A TYR 4.3 2.0 - - - -
142A VAL* 3.5 44.2 - - + +
149A HIS* 3.9 20.0 - - + +
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Residues in contact with GLY 39 (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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37A SER* 3.6 3.0 + - - -
38A LEU* 1.3 82.1 - - - +
40A ARG* 1.3 64.3 + - - -
139A HIS* 3.3 9.8 - - - +
140A HIS* 2.8 31.5 + - - +
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Residues in contact with ARG 40 (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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39A GLY* 1.3 72.5 - - - -
41A ALA* 1.3 77.5 + - - +
42A ASP* 3.4 2.1 + - - -
126A ILE* 4.4 3.0 - - - +
130A GLU* 2.7 41.6 + - - -
136A ALA 5.3 0.2 + - - -
137A GLU* 3.4 21.8 + - - +
138A PHE 3.0 19.3 + - - +
139A HIS* 3.6 31.5 + - + -
140A HIS* 4.4 3.8 - - - -
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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