Contacts of the helix formed by residues 1099 - 1103 (chain I) in PDB entry 6ALG
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 ASN1099 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804I PHE* 4.9 3.6 - - - -
806I PRO* 4.2 1.6 - - - +
811I ASN* 2.5 36.1 + - + +
812I PHE 2.9 18.6 + - - -
813I GLU 3.7 5.8 + - - +
814I ASP* 5.5 2.0 - - - -
815I SER 4.8 5.4 + - - +
1098I LEU* 1.3 83.2 - - - +
1100I PRO* 1.3 74.5 - - - +
1101I LEU* 3.3 11.0 + - - +
1102I GLY* 3.6 10.3 + - - +
1103I VAL* 5.0 2.4 + - - +
1111I GLN* 5.7 1.2 + - - -
504J GLN* 3.4 12.7 - - - +
505J ASP* 3.0 25.8 + - - +
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Residues in contact with PRO1100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804I PHE* 3.5 27.6 - - + +
805I MET* 3.7 21.5 - - - +
806I PRO* 3.7 5.2 - - + -
1099I ASN* 1.3 92.3 - - - +
1101I LEU* 1.3 60.6 + - + +
1102I GLY 3.1 0.4 - - - -
1103I VAL* 3.1 24.9 + - + +
1104I PRO* 3.6 4.5 - - - +
637J ALA 3.4 26.5 - - - +
638J SER* 4.1 2.0 - - - -
639J VAL* 4.0 22.0 - - + +
725J MET* 3.9 11.1 - - - +
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Residues in contact with LEU1101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099I ASN* 3.2 8.1 - - - +
1100I PRO* 1.3 77.1 - - + +
1102I GLY* 1.3 59.6 + - - +
1103I VAL 3.1 1.2 + - - -
1104I PRO* 3.5 8.1 - - - +
1105I SER 4.4 1.0 + - - -
1106I ARG* 5.1 0.7 - - - -
504J GLN* 3.3 48.7 - - + +
505J ASP* 3.2 25.6 - - - +
508J LEU* 4.2 11.7 - - + -
725J MET* 3.6 35.7 - - + -
730J ALA* 4.1 9.6 - - + -
731J ARG* 3.3 41.0 + - + +
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Residues in contact with GLY1102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813I GLU 5.6 0.4 + - - -
814I ASP* 4.8 4.7 + - - -
1099I ASN* 3.6 11.0 + - - +
1100I PRO 3.1 2.2 - - - -
1101I LEU* 1.3 77.2 - - - +
1103I VAL* 1.3 59.5 + - - +
1106I ARG* 3.2 53.6 - - - +
1108I ASN* 3.8 4.1 + - - +
1111I GLN* 4.9 3.1 - - - -
504J GLN* 5.4 1.0 - - - +
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Residues in contact with VAL1103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804I PHE* 5.4 3.8 - - + -
1099I ASN 5.2 1.3 - - - +
1100I PRO* 3.1 18.9 + - + +
1102I GLY* 1.3 77.2 - - - +
1104I PRO* 1.3 68.5 - - + +
1106I ARG 2.8 19.9 - - - +
1107I MET* 3.9 4.7 - - - -
1108I ASN* 4.2 7.8 + - - +
1109I ILE* 3.7 18.6 - - + -
1111I GLN* 3.4 25.1 - - + +
1112I ILE* 3.7 27.6 - - + -
639J VAL* 3.9 24.0 - - + -
722J ILE* 5.5 0.7 - - + -
740J LEU* 4.5 5.1 - - + +
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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