Contacts of the helix formed by residues 1064 - 1077 (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 ALA1064 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050B LEU* 3.8 21.1 - - + +
1051B ASN* 5.6 0.4 - - - -
1054B ALA* 4.2 12.1 - - + -
1059B ILE* 4.7 2.5 - - - -
1060B PRO 3.2 4.9 + - - -
1061B GLN* 3.0 33.7 + - - +
1063B LYS* 1.3 76.9 - - - +
1065B PRO* 1.4 60.8 - - + +
1067B LEU* 3.2 10.2 + - - +
1068B SER* 2.8 28.2 + - - -
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Residues in contact with PRO1065 (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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1050B LEU* 5.4 1.1 - - + -
1061B GLN 3.6 5.2 - - - +
1062B THR 3.5 14.4 - - - +
1063B LYS 3.4 4.3 - - - -
1064B ALA* 1.4 92.6 - - + +
1066B PHE* 1.3 68.0 + - + +
1068B SER* 3.4 8.4 + - - -
1069B ARG* 3.2 30.7 + - - +
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Residues in contact with PHE1066 (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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137A TRP* 3.6 29.8 - + + -
138A LEU* 3.7 16.2 - - + -
149A PRO 4.8 6.3 - - - -
327A MET* 3.7 36.3 - - + +
331A GLU 6.5 1.3 - - - -
1062B THR 4.4 10.1 - - - -
1063B LYS* 3.0 31.1 + - + +
1065B PRO* 1.3 80.4 - - + +
1067B LEU* 1.3 66.4 + - - +
1069B ARG* 3.2 25.2 + - - +
1070B LEU* 3.0 22.5 + - - +
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Residues in contact with LEU1067 (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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138A LEU* 4.4 4.8 - - + +
1035B LEU* 5.2 0.4 - - + -
1037B ILE* 4.5 7.4 - - + -
1050B LEU* 4.0 14.4 - - + -
1053B LEU* 4.1 4.9 - - + -
1054B ALA* 3.6 41.1 - - + +
1057B LEU* 3.9 27.6 - - + -
1059B ILE* 4.0 18.2 - - + -
1063B LYS 3.2 10.4 + - - +
1064B ALA* 3.5 8.7 - - - +
1066B PHE* 1.3 77.1 - - - +
1068B SER* 1.3 57.5 + - - +
1070B LEU* 3.2 13.9 + - + +
1071B MET* 2.8 51.4 + - + +
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Residues in contact with SER1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050B LEU* 3.9 17.6 - - - +
1064B ALA 2.8 13.9 + - - -
1065B PRO* 3.5 12.8 - - - -
1067B LEU* 1.3 75.3 - - - +
1069B ARG* 1.3 59.2 + - - +
1071B MET* 3.3 3.5 + - - +
1072B ARG* 2.9 27.9 + - - +
1082B GLN* 4.9 0.5 - - - +
1096B PRO* 4.3 8.7 - - - +
1098B TYR* 3.6 19.8 + - - -
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Residues in contact with ARG1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 5.9 0.3 - - - +
323A ASP* 3.0 57.5 + - - +
324A MET* 3.4 15.2 - - + +
327A MET* 3.4 15.8 - - - +
332A GLY 2.9 26.9 + - - -
333A SER* 3.5 15.6 - - - +
1065B PRO* 3.2 18.1 + - - +
1066B PHE* 3.2 34.7 + - - +
1068B SER* 1.3 75.9 - - - +
1070B LEU* 1.3 64.7 + - - +
1072B ARG* 3.3 22.4 + - - +
1073B MET* 3.1 17.3 + - - +
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Residues in contact with LEU1070 (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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131A TRP* 5.3 3.6 - - + -
134A MET* 6.1 0.9 - - + -
138A LEU* 4.3 14.6 - - + -
324A MET* 3.7 14.9 - - - +
327A MET* 4.7 6.5 - - + -
1028B THR* 4.0 37.9 - - + +
1031B CYS* 4.4 11.7 - - + -
1032B ALA 5.1 0.2 - - - +
1035B LEU* 4.2 16.4 - - + -
1037B ILE* 4.2 22.4 - - + -
1066B PHE 3.0 13.6 + - - +
1067B LEU* 3.5 13.5 - - + +
1069B ARG* 1.3 75.6 - - - +
1071B MET* 1.3 63.9 + - - +
1073B MET* 3.2 5.5 + - - +
1074B LEU* 3.0 33.7 + - + +
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Residues in contact with MET1071 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037B ILE* 3.8 32.1 - - - -
1041B ILE* 3.9 16.8 - - + -
1053B LEU* 4.0 7.6 - - + -
1067B LEU* 2.8 29.9 + - + +
1068B SER 3.5 3.4 - - - +
1070B LEU* 1.3 77.9 - - - +
1072B ARG* 1.3 56.9 + - - +
1074B LEU* 3.1 9.0 + - - +
1075B VAL* 2.8 35.5 + - - +
1080B PHE* 3.7 27.1 - - + -
1082B GLN* 4.3 0.2 - - - -
1098B TYR* 3.4 55.9 - - + -
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Residues in contact with ARG1072 (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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305A LEU* 3.3 29.2 - - - +
316A MET* 6.3 0.4 - - - -
320A LEU* 3.6 25.9 - - + +
323A ASP* 3.2 31.7 + - - +
333A SER* 5.8 0.4 - - - -
334A LEU 4.2 5.7 + - - -
336A THR* 4.2 13.3 - - - +
339A GLN* 5.2 3.8 + - - +
1068B SER 2.9 14.8 + - - +
1069B ARG* 3.3 23.7 + - - +
1071B MET* 1.3 75.0 - - - +
1073B MET* 1.3 61.9 + - - +
1075B VAL* 3.5 4.3 + - + +
1076B HIS* 3.1 21.5 + - - +
1082B GLN* 3.7 25.7 + - - +
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Residues in contact with MET1073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLY 5.1 0.9 - - - +
320A LEU* 4.1 37.0 - - + +
321A ILE* 3.8 16.2 - - + -
324A MET* 4.0 19.5 - - + -
1024B ILE* 4.2 12.1 - - + -
1025B ASN* 3.0 28.7 - - - +
1028B THR* 3.7 27.6 - - + +
1069B ARG 3.1 11.8 + - - +
1070B LEU 3.4 8.7 - - - +
1072B ARG* 1.3 78.6 - - - +
1074B LEU* 1.3 59.0 + - - +
1076B HIS* 3.2 8.9 + - - +
1077B LEU* 3.0 37.5 + - + +
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Residues in contact with LEU1074 (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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1028B THR* 4.0 18.2 - - - +
1029B LEU* 4.4 4.7 - - + -
1032B ALA* 3.7 32.5 - - + -
1037B ILE* 4.1 12.1 - - + -
1070B LEU* 3.0 39.6 + - + +
1071B MET* 3.1 9.2 + - - +
1073B MET* 1.3 74.1 - - + +
1075B VAL* 1.3 63.8 + - - +
1077B LEU* 3.4 20.5 + - + +
1078B GLY 3.2 4.9 + - - -
1079B TYR* 3.1 34.4 + - + +
1080B PHE* 3.7 24.0 - - + -
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Residues in contact with VAL1075 (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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1071B MET* 2.8 20.6 + - + +
1072B ARG* 3.6 7.2 - - + +
1073B MET 3.3 0.2 - - - -
1074B LEU* 1.3 74.1 - - - +
1076B HIS* 1.3 65.8 + - - +
1078B GLY* 3.0 15.2 + - - -
1080B PHE* 3.4 38.1 - - + +
1081B THR* 4.0 17.0 - - - +
1082B GLN* 3.7 28.3 - - + +
1098B TYR* 4.7 3.4 - - + -
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Residues in contact with HIS1076 (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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313A SER* 3.3 32.0 + - - -
316A MET* 4.0 14.2 - - + +
317A GLY* 3.2 29.4 - - - -
320A LEU* 3.5 26.0 - - + -
401A GOL 3.7 18.9 + - - -
1072B ARG 3.1 6.8 + - - +
1073B MET* 3.2 11.0 + - - +
1075B VAL* 1.3 79.0 - - - +
1077B LEU* 1.3 67.7 + - + +
1078B GLY* 3.2 1.6 + - - -
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Residues in contact with LEU1077 (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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15A GLN* 5.5 1.6 + - - -
19A HIS* 3.2 40.8 + - + +
401A GOL 3.7 32.8 - - - +
1025B ASN* 3.8 19.3 - - - +
1028B THR* 4.1 19.3 - - - +
1029B LEU* 5.3 1.8 - - + -
1073B MET* 3.0 29.0 + - + +
1074B LEU* 3.7 19.7 - - + +
1075B VAL 3.2 0.4 - - - -
1076B HIS* 1.3 79.3 - - + +
1078B GLY* 1.3 58.2 + - - +
1079B TYR* 3.7 17.9 - - + -
1103B LEU* 3.9 6.1 - - - +
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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