Contacts of the helix formed by residues 1100 - 1107 (chain D) in PDB entry 3CMT
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 ASP1100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1077D LEU* 5.8 0.2 - - - +
1098D ALA 3.5 4.3 + - - +
1099D LEU* 1.3 78.1 - - - +
1101D PRO* 1.3 70.9 - - - +
1102D ILE* 3.2 22.4 + - - +
1103D TYR* 3.0 28.0 + - + +
1104D ALA* 2.9 21.0 + - - +
1502D ADP 3.6 8.7 + - - +
2037D VAL* 4.1 21.5 + - + +
2060D ARG* 4.7 3.1 - - - +
2250D LYS 4.4 14.0 - - - +
2251D ILE* 4.2 9.8 - - - +
2330D ASN* 5.5 2.4 + - - -
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Residues in contact with PRO1101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099D LEU* 3.4 11.6 - - - +
1100D ASP* 1.3 87.0 - - - +
1102D ILE* 1.3 70.3 + - + +
1104D ALA* 3.1 4.6 + - + +
1105D ARG* 2.9 26.3 + - - +
1111D ILE* 3.5 16.0 - - + +
2029D LEU* 3.7 36.6 - - + +
2030D GLY* 5.8 0.4 - - - -
2032D ASP 5.6 0.4 - - - +
2035D MET* 3.5 37.5 - - + +
2036D ASP* 4.4 7.6 - - - +
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Residues in contact with ILE1102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100D ASP* 3.2 14.9 + - - +
1101D PRO* 1.3 91.9 - - + +
1103D TYR* 1.3 62.8 + - - +
1105D ARG* 3.4 31.1 + - - +
1106D LYS* 3.1 43.1 + - - +
2036D ASP* 4.5 14.4 - - - +
2037D VAL 6.1 0.9 - - - +
2330D ASN* 5.5 3.4 - - - +
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Residues in contact with TYR1103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074D THR* 3.9 16.8 + - - +
1077D LEU* 4.9 7.0 - - + -
1100D ASP* 3.0 17.3 + - + +
1102D ILE* 1.3 78.1 - - - +
1104D ALA* 1.3 66.9 + - - +
1106D LYS* 3.0 14.1 + - + +
1107D LEU* 3.0 53.6 + - + +
1262D ILE* 4.9 2.8 - - - +
1263D LEU 4.7 1.4 + - - -
1264D TYR* 4.2 4.3 - - - -
1265D GLY* 3.4 38.6 + - - -
1502D ADP 3.2 73.1 + + - +
2330D ASN* 6.0 1.1 - - - -
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Residues in contact with ALA1104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077D LEU* 4.2 33.6 - - + +
1099D LEU* 4.5 2.7 - - + -
1100D ASP 2.9 12.7 + - - +
1101D PRO* 3.1 12.1 + - + +
1103D TYR* 1.3 77.1 - - - +
1105D ARG* 1.3 61.9 + - - +
1107D LEU* 3.2 8.3 + - - +
1109D VAL* 3.0 28.1 + - + +
1111D ILE* 3.6 15.5 - - + -
2029D LEU* 4.4 7.2 - - + -
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Residues in contact with ARG1105 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101D PRO 2.9 9.0 + - - +
1102D ILE* 3.5 33.1 + - - +
1104D ALA* 1.3 77.0 - - - +
1106D LYS* 1.3 58.9 + - - +
1108D GLY* 2.8 21.7 + - - -
1109D VAL 3.7 13.4 + - - +
1111D ILE* 3.5 27.4 - - + +
1112D ASP* 6.0 0.8 + - - -
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Residues in contact with LYS1106 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102D ILE* 3.1 31.1 + - - +
1103D TYR* 3.0 22.5 + - + +
1105D ARG* 1.3 78.0 - - - +
1107D LEU* 1.3 56.8 + - - +
1108D GLY* 3.3 3.6 + - - -
1265D GLY* 3.6 38.6 - - - +
1266D GLU* 3.9 6.2 - - - +
2329D SER 5.1 4.6 + - - -
2330D ASN* 3.6 26.2 - - - +
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Residues in contact with LEU1107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074D THR* 3.9 21.3 - - + +
1077D LEU* 3.8 28.7 - - + -
1078D GLN* 3.0 26.1 + - - +
1081D ALA* 3.9 6.5 - - - +
1085D ARG* 5.5 0.9 + - - -
1103D TYR* 3.0 52.3 + - + +
1104D ALA* 3.6 7.4 - - - +
1105D ARG 3.1 0.8 - - - -
1106D LYS* 1.3 76.5 - - - +
1108D GLY* 1.3 60.0 + - - +
1109D VAL* 3.5 5.4 - - + -
1266D GLU 3.7 9.4 - - - +
1267D GLY* 3.5 32.5 - - - +
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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