Contacts of the helix formed by residues 98 - 108 (chain A) in PDB entry 4H1S
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 GLY 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TYR* 3.8 25.5 - - - -
93A PHE* 3.7 2.0 - - - -
97A LYS* 1.3 73.0 - - - +
99A ALA* 1.3 64.7 + - - +
100A GLU* 2.7 23.6 + - - -
101A VAL* 3.0 14.2 + - - +
102A ALA* 3.1 14.2 + - - +
130A PRO* 3.9 10.0 - - - +
131A LEU* 4.9 0.9 - - - +
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Residues in contact with ALA 99 (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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96A TYR* 2.9 20.7 + - + +
97A LYS 3.4 1.4 + - - -
98A GLY* 1.3 76.6 - - - +
100A GLU* 1.3 56.5 + - - +
102A ALA* 4.1 2.5 - - - +
103A HIS* 3.1 30.8 + - - +
130A PRO* 3.9 16.1 - - + +
134A GLU* 6.3 0.9 - - - -
327A TRP* 4.1 10.1 - - + -
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Residues in contact with GLU 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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39A SER* 4.7 2.1 + - - -
41A LEU* 4.2 23.4 - - + +
92A TRP* 3.7 32.1 - - + +
93A PHE* 3.2 35.5 + - - +
96A TYR* 3.2 18.7 - - + +
98A GLY* 2.7 19.8 + - - -
99A ALA* 1.3 72.3 + - - +
101A VAL* 1.3 74.8 + - + +
103A HIS* 4.4 0.2 - - - -
104A PHE* 3.0 33.4 + - + +
327A TRP* 3.8 17.7 - - + -
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Residues in contact with VAL 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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39A SER* 5.9 0.7 - - - -
41A LEU* 5.4 7.6 - - + -
86A GLN* 3.8 37.9 - - + +
87A TYR* 4.1 17.7 - - + -
93A PHE* 4.7 1.6 - - + -
98A GLY* 3.0 15.2 + - - +
100A GLU* 1.3 94.4 - - + +
102A ALA* 1.3 66.6 + - - +
104A PHE* 4.0 0.6 - - - +
105A MET* 2.9 58.0 + - + +
131A LEU* 4.1 7.9 - - + -
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Residues in contact with ALA 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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98A GLY 3.1 6.8 + - - +
99A ALA* 4.1 3.4 - - - +
101A VAL* 1.3 78.5 - - - +
103A HIS* 1.3 64.4 + - - +
105A MET* 4.6 3.1 - - - -
106A ASN* 2.9 33.1 + - - +
130A PRO 3.8 12.6 - - - +
131A LEU* 4.1 16.6 - - + +
134A GLU* 3.7 36.6 - - + -
135A ALA* 4.3 2.2 - - - +
137A PHE* 5.4 0.2 - - - -
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Residues in contact with HIS 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 ALA 3.1 19.7 + - - +
100A GLU 3.8 2.9 - - - +
102A ALA* 1.3 77.5 - - - +
104A PHE* 1.3 86.4 + + - +
106A ASN* 3.4 7.1 + - - +
107A ALA* 3.0 27.4 + - + +
323A ASP* 2.5 32.4 + - - -
327A TRP* 3.5 26.3 + + + -
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Residues in contact with PHE 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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41A LEU* 3.6 24.2 - - + -
61A VAL* 4.0 21.1 - - + -
92A TRP* 4.4 7.6 - + - -
100A GLU* 3.0 28.3 + - + +
101A VAL 4.5 0.2 - - - +
103A HIS* 1.3 92.2 - + - +
105A MET* 1.3 61.5 + - + +
107A ALA* 3.3 7.5 + - + +
108A LEU* 3.0 34.6 + - - +
320A ILE* 4.1 13.0 - - + -
323A ASP* 3.8 28.9 - - + -
324A ILE* 3.4 42.0 - - + -
327A TRP* 4.3 18.4 - + - -
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Residues in contact with MET 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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82A ASP* 5.0 3.1 - - - -
86A GLN* 3.5 36.8 - - - +
101A VAL* 2.9 39.6 + - + +
102A ALA* 4.2 0.7 - - - +
104A PHE* 1.3 76.3 - - - +
106A ASN* 1.3 61.0 + - - +
108A LEU 3.2 1.2 + - - -
109A ARG 3.0 15.9 + - - -
110A TYR* 3.2 39.5 + - + +
113A MET* 3.6 22.4 - - - +
131A LEU* 3.6 13.2 - - + -
137A PHE* 3.2 41.0 - - + -
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Residues in contact with ASN 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 ALA* 2.9 27.8 + - - +
103A HIS* 3.5 7.0 - - - +
105A MET* 1.3 77.2 - - - +
107A ALA* 1.3 57.5 + - - +
109A ARG* 3.0 26.9 + - - +
134A GLU* 3.1 24.7 + - - +
135A ALA* 3.7 0.6 - - - -
136A LYS* 2.8 61.7 + - + +
137A PHE* 3.2 14.8 - - - -
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Residues in contact with ALA 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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65A PHE* 3.6 19.1 - - - -
103A HIS* 3.0 21.9 + - + +
104A PHE* 3.7 14.4 - - + +
105A MET 3.3 0.4 - - - -
106A ASN* 1.3 76.7 - - - +
108A LEU* 1.3 62.1 + - + +
109A ARG* 3.1 7.8 + - - +
320A ILE* 4.0 22.0 - - + -
323A ASP* 5.6 1.6 - - - +
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Residues in contact with LEU 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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61A VAL* 3.4 33.4 - - + -
64A LEU* 3.5 35.7 - - + -
65A PHE* 3.8 39.9 - - + -
68A VAL* 4.7 2.7 - - + +
72A ARG* 3.2 19.7 + - - -
80A LEU* 3.6 10.2 - - + +
104A PHE 3.0 15.7 + - - +
105A MET 3.7 4.5 - - - +
106A ASN 3.2 0.2 - - - -
107A ALA* 1.3 76.1 - - - +
109A ARG* 1.3 70.2 + - - +
110A TYR* 3.5 21.0 + - + -
320A ILE* 4.5 6.3 - - + -
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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