Contacts of the helix formed by residues 4 - 15 (chain 7) in PDB entry 4E2I
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 4 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27 SER* 3.5 12.4 + - - -
37 ALA* 1.3 88.6 - - - +
57 ALA* 1.3 58.5 + - - +
67 GLN* 2.9 16.3 + - - +
77 GLN* 2.8 43.4 + - - +
87 LEU* 3.6 2.6 + - - +
287 VAL* 4.4 1.2 - - - +
387 GLU* 4.5 0.7 - - - +
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Residues in contact with ALA 5 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47 SER* 1.3 71.6 - - - +
67 GLN* 1.3 56.1 + - + +
77 GLN 3.1 0.4 - - - -
87 LEU* 4.5 3.4 - - - +
97 ALA* 2.7 38.4 + - - +
247 ILE* 3.5 26.2 - - + +
257 GLU* 4.4 11.7 - - + -
287 VAL* 3.6 26.4 - - + +
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Residues in contact with GLN 6 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 SER* 2.9 10.6 + - - +
57 ALA* 1.3 81.6 - - + +
77 GLN* 1.3 59.3 + - + +
97 ALA* 4.1 6.5 - - - -
107 GLU* 3.0 33.0 + - - +
548G ARG* 4.8 2.5 + - - -
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Residues in contact with GLN 7 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37 ALA 3.1 17.0 - - - +
47 SER* 2.8 23.4 + - - +
67 GLN* 1.3 80.1 - - + +
87 LEU* 1.3 61.7 + - - +
107 GLU* 4.0 11.7 - - - +
117 GLU* 4.6 6.2 - - - +
387 GLU* 3.6 29.3 - - + +
397 GLU* 5.4 2.0 - - - +
548G ARG* 4.2 28.1 + - - +
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Residues in contact with LEU 8 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37 ALA* 5.9 0.4 - - + -
47 SER 3.6 2.1 + - - +
57 ALA* 3.2 11.1 + - - +
77 GLN* 1.3 76.3 - - - +
97 ALA* 1.3 65.5 + - - +
107 GLU 3.2 2.0 - - - -
117 GLU* 3.3 14.8 + - - +
127 LEU* 3.4 24.8 - - + +
247 ILE* 4.6 4.7 - - + +
277 LEU* 3.6 41.1 - - + +
287 VAL* 4.5 3.8 - - + +
317 CYS* 3.6 28.7 - - - -
387 GLU* 3.7 20.9 - - + -
417 MET* 4.5 7.2 - - + -
427 VAL* 3.9 22.0 - - + -
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Residues in contact with ALA 9 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57 ALA 2.7 20.3 + - - +
67 GLN* 4.3 7.0 - - - +
87 LEU* 1.3 76.8 - - - +
107 GLU* 1.3 61.7 + - - +
127 LEU* 2.8 32.1 + - + +
137 GLN* 3.2 24.9 + - + +
247 ILE* 3.9 23.8 - - + +
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Residues in contact with GLU 10 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67 GLN* 3.0 26.3 - - - +
77 GLN 4.0 7.0 - - - +
87 LEU 3.2 0.2 - - - -
97 ALA* 1.3 79.3 - - - +
117 GLU* 1.3 66.3 + - - +
137 GLN* 3.1 37.4 + - - +
147 ILE* 3.1 19.5 + - + +
399G PRO* 4.3 22.5 - - + +
548G ARG* 3.8 27.1 - - - +
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Residues in contact with GLU 11 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 GLN 4.6 8.2 - - - +
87 LEU 3.3 4.7 + - - +
97 ALA 3.2 0.8 - - - -
107 GLU* 1.3 80.6 - - - +
127 LEU* 1.3 60.0 + - - +
137 GLN 3.3 0.4 - - - -
147 ILE* 3.6 19.9 + - - +
157 PHE* 3.1 39.0 - - - -
177 LEU* 4.2 0.9 - - - +
387 GLU 4.2 9.6 - - - +
397 GLU* 5.1 7.2 - - + +
427 VAL* 3.5 38.7 - - + +
550G LYS* 4.2 10.2 - - - +
552G TYR* 3.0 44.6 + - - -
620G ALA* 5.9 0.2 - - - -
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Residues in contact with LEU 12 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87 LEU* 3.4 30.1 - - + +
97 ALA* 2.8 24.1 + - - +
117 GLU* 1.3 79.5 - - - +
137 GLN* 1.3 58.1 - - + +
147 ILE 3.3 1.3 - - - -
167 GLY* 3.6 0.9 - - - -
177 LEU* 2.7 71.3 + - + +
197 CYS* 4.2 15.9 - - + -
247 ILE* 3.8 28.0 - - + -
277 LEU* 5.8 5.4 - - + -
427 VAL* 4.7 6.3 - - + -
457 LEU* 6.3 2.2 - - + -
577 LEU* 5.1 1.8 - - + -
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Residues in contact with GLN 13 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97 ALA* 3.4 22.4 + - + +
107 GLU* 3.1 35.8 + - - +
127 LEU* 1.3 78.5 - - + +
147 ILE* 1.3 63.7 - - + +
157 PHE 3.7 0.2 - - - -
167 GLY* 4.0 6.8 + - - +
399G PRO* 6.3 3.1 - - + -
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Residues in contact with ILE 14 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107 GLU* 3.1 20.9 - - + +
117 GLU* 3.6 35.7 - - - +
127 LEU 3.3 0.4 - - - -
137 GLN* 1.3 82.7 - - - +
157 PHE* 1.3 78.6 + - + +
167 GLY 3.2 2.1 + - - -
395G HIS* 4.3 24.0 - - + +
396G CYS* 4.2 17.5 - - - +
398G LEU 5.9 0.9 - - - +
399G PRO* 5.4 17.5 - - + -
550G LYS* 4.7 8.3 - - - +
552G TYR* 3.9 13.0 - - + +
616G LYS* 4.3 13.9 + - - +
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Residues in contact with PHE 15 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117 GLU* 3.1 39.8 + - - -
147 ILE* 1.3 94.8 - - + +
167 GLY* 1.3 64.5 + - - +
177 LEU* 3.9 18.9 - - + +
427 VAL* 4.0 9.2 - - + -
467 ILE* 3.5 22.9 - - + -
396G CYS* 4.1 11.7 - - - -
552G TYR* 5.1 3.8 - + - -
616G LYS* 3.6 31.9 - - + -
617G PHE* 5.4 1.6 - - - -
620G ALA* 3.1 31.2 - - + -
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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