Contacts of the helix formed by residues 103 - 108 (chain A) in PDB entry 1S6L
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 PHE 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 6.0 4.0 - - + -
102A ILE* 1.3 103.9 - - + +
104A PRO* 1.3 63.2 - - + +
105A ALA* 3.3 6.5 - - + -
106A LEU* 3.1 40.4 + - + -
107A ILE* 2.7 34.0 + - + +
200A ASN* 2.9 43.3 - - + -
203A LEU* 4.4 22.7 - - + -
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Residues in contact with PRO 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 5.9 2.0 - - + -
101A LEU* 4.0 17.2 - - + -
102A ILE 4.0 4.7 - - - +
103A PHE* 1.3 88.3 - - + +
105A ALA* 1.3 65.2 + - + +
107A ILE* 3.1 27.5 + - + +
108A GLY 3.4 4.9 + - - -
109A ARG 4.1 2.1 - - - +
111A ALA* 5.2 5.6 - - + -
128A VAL* 3.3 39.5 - - + +
129A SER 3.9 10.5 - - - +
130A PRO* 3.9 9.9 - - - +
193A PHE* 4.1 14.8 - - + -
197A GLN* 6.1 0.7 - - - +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 3.3 5.8 - - + -
104A PRO* 1.3 82.5 - - + +
106A LEU* 1.3 61.6 + - - +
107A ILE 3.6 0.2 + - - -
108A GLY* 4.0 6.9 + - - -
130A PRO* 3.6 33.3 - - + +
197A GLN* 4.7 13.5 - - - +
200A ASN* 6.0 3.6 - - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.3 27.9 - - + +
25A VAL* 5.5 12.6 - - + -
28A LEU* 4.2 29.8 - - + -
103A PHE* 3.1 40.5 + - + +
105A ALA* 1.3 76.8 - - - +
107A ILE* 1.3 69.0 + - + +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 6.6 0.2 - - + -
32A ALA* 4.8 22.8 - - + +
85A PHE* 6.2 3.6 - - + -
87A ILE* 5.1 20.2 - - + -
103A PHE* 2.7 30.1 - - + +
104A PRO* 3.1 18.8 + - + +
106A LEU* 1.3 83.0 - - + +
108A GLY* 1.3 60.3 + - - +
109A ARG* 3.9 21.4 - - + +
110A THR 5.9 0.4 - - - +
111A ALA* 6.1 3.8 - - + -
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PRO 3.4 5.3 + - - -
105A ALA 4.0 5.7 + - - -
106A LEU 3.5 1.2 - - - -
107A ILE* 1.3 79.8 - - - +
109A ARG* 1.3 73.7 + - - +
130A PRO* 3.8 13.5 - - - -
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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