Contacts of the helix formed by residues 1038 - 1044 (chain B) in PDB entry 1Q6S
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 PRO1038 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036B LYS 3.2 6.7 - - - +
1037B LEU* 1.3 89.7 - - + +
1039B LYS* 1.3 61.2 + - - +
1040B ASN 3.1 1.4 + - - -
1041B LYS* 3.2 22.4 + - + +
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Residues in contact with LYS1039 (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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1034B VAL* 5.6 1.4 - - - +
1037B LEU* 3.1 28.6 + - + +
1038B PRO* 1.3 79.4 - - - +
1040B ASN* 1.3 78.7 + - - +
1041B LYS 3.5 0.4 - - - -
1042B ASN* 4.0 12.9 + - - +
1043B ARG* 5.0 1.7 + - - -
1064B ASN* 4.0 29.4 + - + +
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Residues in contact with ASN1040 (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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1034B VAL* 2.9 28.3 + - - +
1035B ALA 3.9 10.3 - - - +
1037B LEU* 2.8 14.6 + - - +
1039B LYS* 1.3 92.5 - - - +
1041B LYS* 1.3 66.4 + - - +
1042B ASN 3.2 2.9 - - - -
1043B ARG* 2.8 21.4 + - - +
1044B ASN* 3.3 12.3 + - - -
1064B ASN* 2.6 33.8 + - - +
1066B TYR* 3.5 32.9 - - + +
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Residues in contact with LYS1041 (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 ALA 5.3 0.4 - - - -
1036B LYS* 5.2 4.5 - - - +
1037B LEU 3.6 3.2 + - - +
1038B PRO* 3.2 19.2 + - + +
1039B LYS 3.5 0.2 - - - -
1040B ASN* 1.3 76.9 - - - +
1042B ASN* 1.3 59.3 + - - +
1043B ARG 3.1 4.5 + - - -
1044B ASN* 3.2 31.7 + - + +
1046B TYR 5.1 1.0 - - - -
1047B ARG* 3.9 38.4 + - - +
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Residues in contact with ASN1042 (chain B).
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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1038B PRO 5.0 0.2 + - - -
1039B LYS 4.0 12.1 + - - +
1041B LYS* 1.3 78.1 - - - +
1043B ARG* 1.3 74.3 + - - +
1044B ASN 3.4 1.3 - - - -
1088B LEU* 3.5 8.6 - - - +
1090B ASN* 2.9 38.2 + - - +
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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 LYS 5.0 1.0 + - - -
1040B ASN* 2.8 26.7 + - - +
1042B ASN* 1.3 91.9 + - - +
1044B ASN* 1.3 64.9 + - - +
1059B LEU* 4.1 2.4 - - - +
1061B GLN* 3.9 5.5 - - - +
1063B ASP* 4.5 4.9 + - - -
1064B ASN* 3.4 48.6 + - - +
1066B TYR* 2.8 47.3 + - + +
1067B ILE* 5.4 1.6 - - - -
1068B ASN* 4.1 6.4 + - - +
1085B GLN* 2.9 20.1 + - - -
1088B LEU* 3.7 3.8 - - - +
1090B ASN* 4.6 1.8 - - - +
1091B THR* 4.0 20.9 - - + +
1094B HIS* 3.3 35.5 + - - +
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Residues in contact with ASN1044 (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 ALA* 3.0 29.1 + - - +
1036B LYS* 5.6 1.6 - - - +
1040B ASN 3.3 15.7 + - - -
1041B LYS* 3.2 24.7 + - + +
1042B ASN* 3.4 0.7 - - - -
1043B ARG* 1.3 80.4 - - - +
1045B ARG* 1.3 65.8 + - - +
1046B TYR* 4.0 17.0 - - - +
1049B VAL 4.9 1.8 - - - -
1050B SER* 4.9 4.3 + - - -
1066B TYR* 2.5 31.1 + - - -
1068B ASN* 3.0 15.5 + - - +
1085B GLN* 3.8 1.8 - - - -
1088B LEU* 3.8 5.8 - - - +
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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