Contacts of the helix formed by residues 4 - 15 (chain 1) 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 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21 SER* 3.5 12.6 + - - -
31 ALA* 1.3 89.0 - - - +
51 ALA* 1.3 58.5 + - - +
61 GLN* 2.9 15.4 + - - -
71 GLN* 2.8 44.6 + - - +
81 LEU* 3.6 2.5 + - - +
281 VAL* 4.4 1.8 - - - +
381 GLU* 4.5 0.5 - - - +
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Residues in contact with ALA 5 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41 SER* 1.3 71.5 - - - +
61 GLN* 1.3 55.1 + - + +
71 GLN 3.1 0.2 - - - -
81 LEU* 3.2 4.2 + - - +
91 ALA* 2.7 38.4 + - - +
241 ILE* 3.5 25.9 - - + +
251 GLU* 4.4 12.3 - - + -
281 VAL* 3.6 25.9 - - + +
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Residues in contact with GLN 6 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41 SER* 2.9 11.4 + - - +
51 ALA* 1.3 81.1 - - + +
71 GLN* 1.3 59.8 + - + +
91 ALA* 4.1 6.3 - - - -
101 GLU* 3.0 32.9 + - - +
548A ARG* 5.0 1.8 + - - -
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Residues in contact with GLN 7 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31 ALA 3.1 17.5 - - - +
41 SER* 2.8 24.1 + - - +
61 GLN* 1.3 80.1 - - + +
81 LEU* 1.3 60.9 + - - +
91 ALA 3.5 0.2 - - - -
101 GLU* 4.1 12.5 - - - +
111 GLU* 4.6 6.1 - - - +
381 GLU* 3.6 29.0 - - + +
391 GLU* 5.4 1.6 - - - +
548A ARG* 3.9 38.2 + - - +
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Residues in contact with LEU 8 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31 ALA* 5.9 0.7 - - + -
41 SER 3.6 2.4 + - - +
51 ALA* 3.2 10.8 + - - +
71 GLN* 1.3 77.2 - - - +
91 ALA* 1.3 65.2 + - - +
101 GLU 3.2 1.8 - - - -
111 GLU* 3.3 14.6 + - - +
121 LEU* 3.4 25.6 - - + +
241 ILE* 4.6 5.6 - - + +
271 LEU* 3.6 41.5 - - + +
281 VAL* 4.5 3.6 - - + +
311 CYS* 3.6 28.0 - - - -
381 GLU* 3.7 20.0 - - + -
411 MET* 4.5 7.4 - - + -
421 VAL* 3.9 21.5 - - + -
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Residues in contact with ALA 9 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 ALA 2.7 20.1 + - - +
61 GLN* 4.3 7.4 - - - +
71 GLN 3.5 0.2 - - - -
81 LEU* 1.3 76.2 - - - +
101 GLU* 1.3 60.2 - - - +
121 LEU* 2.8 31.5 + - + +
131 GLN* 3.2 26.1 + - + +
241 ILE* 3.8 24.2 - - + +
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Residues in contact with GLU 10 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61 GLN* 3.0 27.4 - - - +
71 GLN* 4.1 11.9 - - - +
81 LEU 3.2 0.2 - - - -
91 ALA* 1.3 79.9 - - - +
111 GLU* 1.3 66.2 + - - +
131 GLN* 3.1 36.1 + - - +
141 ILE* 3.1 19.0 + - + +
399A PRO* 3.1 37.3 - - + +
548A ARG* 4.5 13.5 - - - +
550A LYS* 6.1 1.8 - - - +
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Residues in contact with GLU 11 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71 GLN 4.6 8.7 - - - +
81 LEU 3.3 4.9 + - - +
91 ALA 3.2 0.4 - - - -
101 GLU* 1.3 79.6 - - - +
121 LEU* 1.3 61.5 + - - +
141 ILE* 3.6 18.2 + - - +
151 PHE* 3.1 38.8 - - - -
171 LEU* 4.2 0.5 - - - +
381 GLU 4.2 9.6 - - - +
391 GLU* 5.1 5.8 - - + +
421 VAL* 3.5 38.7 - - + +
550A LYS* 4.1 10.2 - - - +
552A TYR* 3.1 49.0 + - - -
620A ALA* 5.7 0.3 - - - -
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Residues in contact with LEU 12 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 LEU* 3.4 29.2 - - + +
91 ALA* 2.8 24.9 + - + +
111 GLU* 1.3 79.7 - - - +
131 GLN* 1.3 58.2 + - + +
141 ILE 3.3 0.9 - - - -
161 GLY* 3.6 0.7 - - - -
171 LEU* 2.7 71.9 + - + +
191 CYS* 4.2 17.3 - - + -
241 ILE* 3.8 26.5 - - + -
271 LEU* 5.8 5.4 - - + -
421 VAL* 4.7 7.4 - - + -
451 LEU* 6.3 2.2 - - + -
571 LEU* 5.1 2.0 - - + -
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Residues in contact with GLN 13 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 ALA* 3.4 21.7 + - + +
101 GLU* 3.1 35.4 + - - +
121 LEU* 1.3 79.1 - - + +
141 ILE* 1.3 63.2 + - + +
161 GLY* 4.0 7.6 + - - +
395A HIS* 4.8 5.7 - - - -
399A PRO* 5.3 9.8 - - + +
400A LYS* 5.1 23.3 + - + +
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Residues in contact with ILE 14 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 GLU* 3.1 20.6 - - + +
111 GLU* 3.6 33.9 - - - +
121 LEU 3.3 0.2 - - - -
131 GLN* 1.3 81.5 - - - +
151 PHE* 1.3 67.2 + - + +
161 GLY 3.2 2.0 + - - -
395A HIS* 3.5 28.8 - - + +
396A CYS* 3.4 35.7 - - + +
398A LEU 5.6 2.5 - - - -
399A PRO* 5.1 13.0 - - + -
400A LYS 6.0 0.7 - - - +
550A LYS* 4.5 6.7 - - - +
552A TYR* 3.8 13.7 - - + +
616A LYS* 2.9 26.4 + - - -
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Residues in contact with PHE 15 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 GLU* 3.1 39.6 + - - -
121 LEU 4.4 0.2 + - - -
141 ILE* 1.3 81.8 - - + +
161 GLY* 1.3 63.7 + - - +
171 LEU* 3.9 19.5 - - + +
421 VAL* 4.0 8.3 - - + -
461 ILE* 3.5 21.8 - - + -
396A CYS* 3.5 22.0 - - - -
552A TYR* 5.0 3.1 - + - -
613A GLN* 4.8 16.6 - - + +
616A LYS* 3.0 42.4 - - + +
617A PHE* 4.7 2.2 - - - -
620A ALA* 3.2 31.9 - - + -
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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