Contacts of the helix formed by residues 1037 - 1044 (chain B) in PDB entry 4E70
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 ILE1037 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032B ALA* 3.1 32.4 + - - +
1035B LEU* 3.8 20.9 - - + -
1036B ASP* 1.3 75.7 - - - +
1038B ALA* 1.3 64.6 + - - +
1040B VAL* 3.2 2.3 + - - +
1041B ILE* 2.9 50.2 + - + +
1053B LEU* 4.8 5.4 - - + -
1057B LEU* 4.1 19.3 - - + -
1067B LEU* 4.5 1.3 - - + -
1070B LEU* 4.2 15.3 - - + -
1071B MET* 3.8 29.4 - - - -
1074B LEU* 4.1 9.2 - - + -
1080B PHE* 3.8 12.6 - - + -
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Residues in contact with ALA1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032B ALA 4.7 1.2 + - - -
1033B LEU* 6.3 0.4 - - + -
1036B ASP 3.4 0.4 - - - -
1037B ILE* 1.3 80.0 - - - +
1039B ASP* 1.3 61.2 + - - +
1041B ILE* 3.4 1.4 + - - +
1042B HIS* 2.8 31.2 + - - +
1080B PHE* 3.8 26.3 - - + -
1100B LEU* 3.8 5.6 - - + +
1104B SER* 4.7 2.2 - - - +
1107B LEU* 3.9 28.5 - - + +
1108B LEU* 3.5 18.3 - - + +
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Residues in contact with ASP1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036B ASP* 3.2 33.1 + - + +
1038B ALA* 1.3 75.2 + - - +
1040B VAL* 1.3 61.6 + - + +
1042B HIS* 3.5 2.2 + - - +
1043B ARG* 2.9 31.1 + - - +
1107B LEU 4.3 4.0 - - - +
1108B LEU* 3.6 12.9 - - - +
1109B LYS* 2.8 51.5 + - + +
1110B GLN 4.7 0.2 + - - -
1116B ARG* 4.2 5.7 + - - -
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Residues in contact with VAL1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035B LEU 4.4 1.8 - - - +
1036B ASP* 3.0 26.3 + - + +
1037B ILE 3.7 3.4 - - - +
1039B ASP* 1.3 73.9 - - + +
1041B ILE* 1.3 66.1 + - - +
1043B ARG* 3.5 27.6 + - - +
1044B HIS* 3.2 21.0 + - - +
1048B ILE* 4.5 5.5 - - + +
1053B LEU* 3.7 19.7 - - + -
1056B ALA* 3.7 30.1 - - + +
1057B LEU* 3.8 18.6 - - + -
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Residues in contact with ILE1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037B ILE* 2.9 37.9 + - + +
1038B ALA 3.7 3.4 - - - +
1040B VAL* 1.3 73.4 - - - +
1042B HIS* 1.3 66.3 + - - +
1044B HIS* 3.0 18.4 + - - +
1048B ILE* 3.8 20.9 - - + -
1053B LEU* 4.1 9.4 - - + -
1071B MET* 3.9 18.4 - - + -
1080B PHE* 3.9 16.4 - - + -
1098B TYR* 3.8 21.3 - - + +
1099B TRP* 3.3 34.5 - - + +
1100B LEU* 3.8 12.3 - - + -
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Residues in contact with HIS1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038B ALA 2.8 18.3 + - - +
1039B ASP* 3.8 3.6 + - - +
1041B ILE* 1.3 75.7 - - - +
1043B ARG* 1.3 66.2 + - - +
1045B GLY* 3.1 15.4 + - - -
1099B TRP* 4.4 7.3 - + - -
1100B LEU* 3.6 26.2 - - + +
1108B LEU* 3.7 25.2 - - + +
1110B GLN* 3.6 35.9 + - - -
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Residues in contact with ARG1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039B ASP 2.9 18.2 + - - +
1040B VAL* 3.7 30.5 + - - +
1042B HIS* 1.3 79.8 + - - +
1044B HIS* 1.3 63.6 + - - +
1045B GLY* 3.2 2.4 + - - -
1056B ALA* 4.0 22.4 + - - +
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Residues in contact with HIS1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B VAL 3.2 12.4 + - - +
1041B ILE 3.0 11.5 + - - +
1043B ARG* 1.3 77.9 - - - +
1045B GLY* 1.3 56.9 + - - +
1046B HIS* 3.2 71.3 + + - +
1047B PRO 3.7 6.1 + - - -
1048B ILE* 3.6 36.9 - - + +
1049B PRO* 4.2 3.6 - - - +
1052B GLN* 3.1 29.7 + - + -
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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