Contacts of the helix formed by residues 4 - 15 (chain 8) 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 8).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28 SER* 3.5 11.2 + - - -
38 ALA* 1.3 89.1 - - - +
58 ALA* 1.3 58.0 + - - +
68 GLN* 2.9 15.9 + - - +
78 GLN* 2.8 43.9 + - - +
88 LEU* 3.6 2.8 + - - +
288 VAL* 4.4 1.8 - - - +
388 GLU* 4.5 0.5 - - - +
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Residues in contact with ALA 5 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48 SER* 1.3 71.8 - - - +
68 GLN* 1.3 54.7 + - + +
88 LEU* 3.7 4.0 - - - +
98 ALA* 2.7 38.3 + - - +
248 ILE* 3.5 26.6 - - + +
258 GLU* 4.4 11.7 - - + -
288 VAL* 3.6 25.7 - - + +
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Residues in contact with GLN 6 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48 SER* 2.9 10.2 + - - +
58 ALA* 1.3 81.5 - - + +
78 GLN* 1.3 58.7 + - + +
98 ALA* 4.1 6.5 - - - -
108 GLU* 3.0 32.9 + - - +
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Residues in contact with GLN 7 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38 ALA 3.1 17.3 - - - +
48 SER* 2.8 24.9 + - - +
68 GLN* 1.3 79.7 - - + +
88 LEU* 1.3 61.2 + - - +
108 GLU* 4.0 8.1 - - - +
118 GLU* 4.6 3.5 - - - +
388 GLU* 3.6 28.7 - - + +
398 GLU* 5.8 1.1 - - - +
548H ARG* 3.7 32.7 + - - +
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Residues in contact with LEU 8 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38 ALA* 5.9 0.9 - - + -
48 SER 3.6 2.3 + - - +
58 ALA* 3.2 11.5 + - - +
78 GLN* 1.3 76.3 - - - +
98 ALA* 1.3 65.8 + - - +
108 GLU 3.2 2.0 - - - -
118 GLU* 3.3 14.8 + - - +
128 LEU* 3.4 25.1 - - + +
248 ILE* 4.6 4.5 - - + +
278 LEU* 3.6 41.1 - - + +
288 VAL* 4.5 3.4 - - + +
318 CYS* 3.6 28.3 - - - -
388 GLU* 3.7 20.9 - - + -
418 MET* 4.5 7.2 - - + -
428 VAL* 3.9 21.1 - - + -
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Residues in contact with ALA 9 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58 ALA 2.7 20.9 + - - +
68 GLN* 4.3 7.2 - - - +
88 LEU* 1.3 75.6 - - - +
108 GLU* 1.3 61.2 + - - +
128 LEU* 2.8 31.6 + - - +
138 GLN* 3.2 25.2 + - + +
248 ILE* 3.8 23.7 - - + +
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Residues in contact with GLU 10 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68 GLN* 3.0 25.8 - - - +
78 GLN 4.0 10.8 - - - +
88 LEU 3.2 0.2 - - - -
98 ALA* 1.3 79.4 - - - +
118 GLU* 1.3 62.5 + - - +
138 GLN* 3.1 36.8 + - - +
148 ILE* 3.1 19.5 + - + +
399H PRO* 4.1 20.1 - - + +
548H ARG* 4.1 24.5 - - - +
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Residues in contact with GLU 11 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78 GLN 4.6 8.3 - - - +
88 LEU 3.3 4.7 + - - +
98 ALA 3.2 0.4 - - - -
108 GLU* 1.3 76.5 - - - +
128 LEU* 1.3 61.2 + - - +
138 GLN 3.3 0.4 + - - -
148 ILE* 3.6 23.8 + - - +
158 PHE* 3.1 34.8 - - - -
178 LEU* 4.2 0.5 - - - +
388 GLU 4.2 9.9 - - - +
398 GLU* 5.1 13.0 - - + +
428 VAL* 3.5 37.9 - - + +
548H ARG* 3.8 19.9 + - - +
550H LYS* 4.1 11.7 - - - +
552H TYR* 3.9 23.7 - - - -
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Residues in contact with LEU 12 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 LEU* 3.4 30.1 - - + +
98 ALA* 2.8 24.5 + - - +
118 GLU* 1.3 80.2 - - - +
138 GLN* 1.3 60.0 + - + +
148 ILE 3.3 1.1 - - - -
168 GLY 3.6 1.1 + - - -
178 LEU* 2.7 71.6 + - + +
198 CYS* 4.2 17.0 - - + -
248 ILE* 3.8 27.8 - - + -
278 LEU* 5.8 6.1 - - + -
428 VAL* 4.7 6.7 - - + -
458 LEU* 6.3 2.2 - - + -
578 LEU* 5.1 1.8 - - + -
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Residues in contact with GLN 13 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 ALA* 3.4 22.6 + - + +
108 GLU* 3.1 36.0 + - - +
128 LEU* 1.3 78.2 - - + +
148 ILE* 1.3 62.7 + - - +
168 GLY* 4.0 6.6 + - - +
395H HIS* 5.0 4.7 - - - -
399H PRO* 4.4 16.4 - - + +
400H LYS* 4.2 29.1 + - + +
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Residues in contact with ILE 14 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108 GLU* 3.1 21.1 - - + +
118 GLU* 3.6 32.1 - - - +
128 LEU 3.3 0.6 - - - -
138 GLN* 1.3 80.9 - - - +
158 PHE* 1.3 67.7 + - + +
168 GLY 3.2 2.1 + - - -
395H HIS* 3.7 26.6 + - - +
396H CYS* 3.4 38.2 - - - +
397H LEU 4.5 0.2 - - - +
398H LEU 4.9 1.1 - - - +
399H PRO* 4.0 21.1 - - + -
550H LYS* 3.1 30.3 - - - +
552H TYR* 3.6 8.1 - - - +
616H LYS* 4.2 5.2 + - - -
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Residues in contact with PHE 15 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118 GLU* 3.1 32.1 + - - -
128 LEU 4.4 0.2 + - - -
148 ILE* 1.3 81.4 - - + +
168 GLY* 1.3 63.4 + - - +
178 LEU* 3.9 18.9 - - + +
428 VAL* 4.0 9.6 - - + -
468 ILE* 3.5 31.9 - - + -
396H CYS* 4.0 17.3 - - - -
552H TYR* 3.3 59.0 - + - -
613H GLN* 6.1 1.4 - - - +
616H LYS* 4.7 13.8 + - + +
620H ALA* 4.2 19.5 - - + -
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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