Contacts of the helix formed by residues 99 - 106 (chain A) in PDB entry 4L6V
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 ASN 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER* 1.3 72.7 - - - +
100A TYR* 1.3 52.5 + - - +
101A GLU 3.3 2.5 - - - -
102A GLY* 3.0 8.3 + - - +
103A TRP* 2.7 32.1 + - - +
110A ILE* 3.5 19.4 - - - +
111A LYS 3.3 21.0 + - - -
113A SER 2.9 27.2 + - - +
130A VAL* 3.9 13.1 - - - +
131A GLY 4.1 4.4 + - - -
134A PHE* 3.6 28.0 - - + -
144A PHE* 3.2 6.4 - - - -
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Residues in contact with TYR 100 (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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94A GLY* 4.1 6.1 - - - +
98A SER* 3.1 17.5 + - - +
99A ASN* 1.3 76.7 - - - +
101A GLU* 1.3 61.0 + - + +
103A TRP* 3.0 13.4 + + - +
104A LEU* 2.7 53.2 + - + +
144A PHE* 3.3 42.3 - + + -
147A TRP* 3.1 41.9 - + + +
148A ARG* 3.2 11.8 + - - +
152A PHE* 2.9 35.0 + - + -
153A THR* 4.5 2.7 - - - -
154A ASP 4.8 5.2 - - - -
155A SER* 5.8 2.0 - - - +
158A LEU* 3.9 15.0 - - + -
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Residues in contact with GLU 101 (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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99A ASN 3.3 0.6 - - - -
100A TYR* 1.3 84.0 - - + +
102A GLY* 1.3 60.8 + - - +
104A LEU* 3.4 9.0 + - - +
105A ALA* 3.4 20.1 + - - +
153A THR 4.8 5.6 - - - +
154A ASP* 3.3 20.1 - - - +
155A SER* 3.0 44.7 + - - +
233A PRO* 5.0 5.7 - - + +
234A LYS* 5.1 8.6 + - - -
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Residues in contact with GLY 102 (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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99A ASN* 3.0 13.2 + - - +
101A GLU* 1.3 79.0 - - - +
103A TRP* 1.3 61.1 + - - +
105A ALA* 3.5 13.8 + - - +
106A ASP* 3.6 8.5 + - - +
110A ILE* 3.8 16.5 - - - +
132A GLY* 6.1 3.4 - - - -
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Residues in contact with TRP 103 (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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99A ASN* 2.7 18.4 + - - +
100A TYR* 3.0 19.2 + + - +
102A GLY* 1.3 71.0 - - - +
104A LEU* 1.3 69.9 + - - +
105A ALA 3.1 2.2 + - - -
106A ASP 3.3 0.2 - - - -
107A PRO* 3.1 50.6 + - + +
110A ILE* 3.3 39.1 + - + +
112A PRO* 4.1 13.8 - - + +
144A PHE* 3.5 41.3 - + + -
145A TYR* 3.5 38.1 - + - -
148A ARG* 3.5 38.6 - - + -
377A PRO* 4.8 1.1 - - + -
378A TYR* 4.4 9.2 - + + -
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Residues in contact with LEU 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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100A TYR* 2.7 32.6 + - + +
101A GLU* 3.8 8.5 - - - +
102A GLY 3.4 0.6 - - - -
103A TRP* 1.3 79.1 - - + +
105A ALA* 1.3 59.9 + - - +
107A PRO* 4.0 9.7 - - - +
148A ARG* 3.7 33.9 + - + +
152A PHE 3.3 26.9 - - - +
153A THR* 3.6 22.4 - - + -
227A LEU* 3.8 25.7 - - + +
233A PRO* 4.3 20.7 - - + +
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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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101A GLU 3.4 10.2 + - - +
102A GLY* 3.7 11.4 - - - +
103A TRP 3.1 0.6 - - - -
104A LEU* 1.3 81.7 - - - +
106A ASP* 1.3 60.5 + - + +
107A PRO* 3.6 4.9 - - - +
232A ALA* 6.1 2.4 - - + +
233A PRO* 4.6 14.8 - - + +
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Residues in contact with ASP 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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102A GLY 3.6 3.5 + - - +
103A TRP 3.3 3.7 + - - -
105A ALA* 1.3 80.9 - - + +
107A PRO* 1.3 64.1 - - - +
108A THR* 3.5 8.1 - - - +
109A HIS* 3.1 46.2 + - - +
110A ILE* 3.2 36.0 + - + +
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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