Contacts of the helix formed by residues 4 - 15 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25 SER* 3.5 13.2 + - - -
35 ALA* 1.3 88.6 - - - +
55 ALA* 1.3 58.7 + - - +
65 GLN* 2.9 15.0 + - - -
75 GLN* 2.8 43.7 + - - +
85 LEU* 3.6 2.6 + - - +
285 VAL* 4.4 1.4 - - - +
385 GLU* 4.5 0.5 - - - +
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Residues in contact with ALA 5 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35 ALA 3.9 0.2 - - - -
45 SER* 1.3 71.5 - - - +
65 GLN* 1.3 54.1 + - + +
75 GLN 3.1 0.2 - - - -
85 LEU* 3.7 4.5 - - - +
95 ALA* 2.7 39.5 + - - +
245 ILE* 3.5 27.2 - - + +
255 GLU* 4.4 11.7 - - + -
285 VAL* 3.6 26.1 - - + +
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Residues in contact with GLN 6 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45 SER* 2.9 11.4 + - - +
55 ALA* 1.3 80.3 - - + +
75 GLN* 1.3 59.9 + - + +
85 LEU 3.4 0.2 - - - -
95 ALA* 4.1 6.3 - - - -
105 GLU* 3.0 33.4 + - - +
548E ARG* 5.4 0.9 + - - -
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Residues in contact with GLN 7 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35 ALA 3.1 16.8 - - - +
45 SER* 2.8 23.1 + - - +
65 GLN* 1.3 80.3 - - + +
85 LEU* 1.3 60.5 + - - +
95 ALA 3.5 0.2 - - - -
105 GLU* 4.0 15.4 - - - +
115 GLU* 4.6 6.4 - - - +
385 GLU* 3.6 28.1 - - + +
395 GLU* 5.4 1.6 - - - +
548E ARG* 4.8 7.0 + - - +
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Residues in contact with LEU 8 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35 ALA* 5.9 0.4 - - + -
45 SER 3.6 1.9 + - - +
55 ALA* 3.2 11.1 + - - +
75 GLN* 1.3 77.0 - - - +
95 ALA* 1.3 65.3 + - - +
105 GLU 3.2 2.2 - - - -
115 GLU* 3.3 14.8 + - - +
125 LEU* 3.4 25.1 - - + +
245 ILE* 4.6 4.9 - - + +
275 LEU* 3.6 40.6 - - + +
285 VAL* 4.5 3.6 - - + +
315 CYS* 3.6 28.7 - - - -
385 GLU* 3.7 20.9 - - + -
415 MET* 4.5 7.0 - - + -
425 VAL* 3.9 21.1 - - + -
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Residues in contact with ALA 9 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55 ALA 2.7 19.8 + - - +
65 GLN* 4.3 7.6 - - - +
75 GLN 3.5 0.2 - - - -
85 LEU* 1.3 76.2 - - - +
105 GLU* 1.3 61.9 + - - +
125 LEU* 2.8 30.7 + - - +
135 GLN* 3.2 26.6 + - + +
245 ILE* 3.9 23.5 - - + +
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Residues in contact with GLU 10 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65 GLN* 3.0 26.7 - - - +
75 GLN 4.0 7.9 - - - +
85 LEU 3.2 0.2 - - - -
95 ALA* 1.3 79.3 - - - +
115 GLU* 1.3 66.5 + - - +
135 GLN* 3.1 38.1 + - - +
145 ILE* 3.1 20.0 + - + +
399E PRO* 5.1 13.4 - - + +
548E ARG* 3.3 40.3 + - - +
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Residues in contact with GLU 11 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75 GLN 4.6 8.9 - - - +
85 LEU 3.6 4.3 - - - +
95 ALA 3.2 0.8 - - - -
105 GLU* 1.3 79.8 - - - +
125 LEU* 1.3 60.7 + - - +
135 GLN 3.3 0.2 - - - -
145 ILE* 3.6 23.9 + - - +
155 PHE* 3.1 37.9 - - - -
175 LEU* 4.2 0.7 - - - +
385 GLU 4.2 9.4 - - - +
395 GLU* 5.1 13.3 - - + +
425 VAL* 3.5 38.0 - - + +
548E ARG* 5.8 1.2 + - - -
550E LYS* 4.5 7.8 - - - +
552E TYR* 3.2 34.7 + - - -
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Residues in contact with LEU 12 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85 LEU* 3.4 30.5 - - + +
95 ALA* 2.8 23.6 + - - +
115 GLU* 1.3 80.5 - - - +
135 GLN* 1.3 59.1 + - + +
145 ILE 3.3 0.9 - - - -
165 GLY 3.6 1.0 + - - -
175 LEU* 2.7 71.7 + - + +
195 CYS* 4.2 16.6 - - + -
245 ILE* 3.8 27.4 - - + -
275 LEU* 5.8 5.4 - - + -
425 VAL* 4.7 7.2 - - + -
455 LEU* 6.3 2.0 - - + -
575 LEU* 5.1 1.8 - - + -
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Residues in contact with GLN 13 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95 ALA* 3.4 22.4 + - + +
105 GLU* 3.1 35.8 + - - +
125 LEU* 1.3 77.8 - - + +
145 ILE* 1.3 64.9 + - + +
165 GLY* 4.0 6.7 + - - -
399E PRO* 5.0 20.1 - - + +
400E LYS* 5.0 8.3 + - - +
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Residues in contact with ILE 14 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105 GLU* 3.1 21.1 - - + +
115 GLU* 3.6 30.5 - - - +
125 LEU 3.3 0.2 - - - -
135 GLN* 1.3 82.1 - - - +
155 PHE* 1.3 75.0 + - + +
165 GLY 3.2 2.1 + - - -
395E HIS* 3.9 27.9 + - - +
396E CYS* 3.8 30.5 - - + -
398E LEU 5.3 2.2 - - - +
399E PRO* 4.8 18.6 - - + -
400E LYS 5.7 0.4 - - - +
550E LYS* 3.9 13.9 - - - +
552E TYR* 3.6 19.7 - - - +
616E LYS* 4.3 4.0 + - - -
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Residues in contact with PHE 15 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 GLU* 3.1 38.5 + - - -
145 ILE* 1.3 88.7 - - + +
165 GLY* 1.3 63.5 + - - +
175 LEU* 3.9 18.3 - - + +
425 VAL* 4.0 10.1 - - + -
465 ILE* 3.5 30.1 - - + -
396E CYS* 3.7 28.5 - - + -
552E TYR* 4.5 8.5 - + - -
613E GLN* 6.1 0.9 - - - +
616E LYS* 4.1 18.4 - - + +
617E PHE* 6.1 0.2 - - - -
620E ALA* 3.5 28.5 - - + -
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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