Contacts of the strand formed by residues 107 - 114 (chain A) in PDB entry 1H1W
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 GLU 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.8 25.4 - - + +
99A ALA 3.3 8.5 - - - +
100A ARG* 3.4 41.7 + - + +
105A SER 4.4 0.4 - - - +
106A ARG* 1.3 74.2 - - - +
108A TYR* 1.3 60.4 + - - +
161A TYR* 4.0 29.1 - - + +
163A LYS* 4.6 10.6 - - - +
1363A GOL 2.9 29.9 + - - +
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Residues in contact with TYR 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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77A LYS* 5.4 2.4 - - - -
82A PHE* 4.1 11.9 - + - -
98A LEU* 3.7 3.9 - - - +
99A ALA* 2.8 33.9 + - - +
101A GLU* 3.8 21.6 + - + -
106A ARG* 3.5 39.6 + - + -
107A GLU* 1.3 74.8 - - - +
109A ALA* 1.3 61.5 + - - +
110A ILE* 3.6 17.3 + - + -
146A TYR* 3.6 36.8 - + + +
147A PHE* 3.9 27.2 - + + -
159A LEU 3.6 13.9 - - - +
161A TYR* 4.3 4.7 - - - -
1363A GOL 3.5 29.4 - - - -
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Residues in contact with ALA 109 (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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88A LEU* 3.8 18.4 - - + -
96A VAL* 3.9 5.4 - - + -
97A VAL 3.7 5.4 - - - -
108A TYR* 1.3 72.2 - - - +
110A ILE* 1.3 61.4 + - - +
157A PHE 3.6 0.3 - - - +
159A LEU* 2.9 34.7 + - + +
160A SER 3.8 5.6 - - - +
161A TYR* 4.1 6.3 - - + +
1373A ATP 3.6 39.5 - - + +
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Residues in contact with ILE 110 (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 PHE* 3.9 33.0 - - + -
84A PHE* 4.0 15.5 - - + -
95A THR 3.6 1.7 - - - +
96A VAL* 3.4 1.6 - - - -
97A VAL* 2.8 40.0 + - - +
99A ALA* 3.6 26.9 - - + -
108A TYR* 4.2 10.8 - - + -
109A ALA* 1.3 74.8 - - - +
111A LYS* 1.3 63.1 + - - +
112A ILE* 3.6 7.3 + - + +
147A PHE* 4.3 5.2 - - + -
149A PHE* 4.8 2.2 - - + -
156A TYR* 3.9 35.7 - - + -
157A PHE 3.3 12.1 - - - +
158A GLY* 4.4 4.5 - - - -
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Residues in contact with LYS 111 (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 SER* 3.7 12.6 - - - +
95A THR 3.6 3.6 - - - -
96A VAL* 4.0 16.8 - - + +
109A ALA 3.7 2.0 + - - -
110A ILE* 1.3 71.1 - - - +
112A ILE* 1.3 62.0 + - - +
113A LEU* 3.6 18.8 - - + +
130A GLU* 2.7 35.2 + - - +
155A LEU 3.6 1.2 - - - +
156A TYR* 3.5 4.3 - - - -
157A PHE* 3.0 37.9 + - + +
159A LEU* 4.1 21.7 - - + +
222A THR* 5.3 4.0 + - - -
223A ASP* 5.2 6.1 + - - +
1366A GOL 2.7 24.3 + - - +
1373A ATP 2.9 31.7 + - - -
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Residues in contact with ILE 112 (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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84A PHE* 4.1 16.4 - - + -
94A SER* 3.2 3.6 - - - -
95A THR* 2.8 41.8 + - - +
97A VAL* 3.9 23.3 - - + -
110A ILE* 3.9 8.5 - - + +
111A LYS* 1.3 76.7 - - - +
113A LEU* 1.3 63.1 + - - +
114A GLU 5.3 0.2 - - - +
154A LYS* 3.5 40.6 - - + +
155A LEU 3.4 4.7 - - - +
156A TYR* 3.8 22.0 - - + -
1360A GOL 3.9 17.0 - - - +
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Residues in contact with LEU 113 (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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93A PHE 3.5 16.8 - - - +
94A SER* 3.6 12.3 - - - +
111A LYS* 3.6 25.8 - - + +
112A ILE* 1.3 78.3 - - - +
114A GLU* 1.3 62.5 + - - +
115A LYS 3.4 1.0 + - - -
118A ILE* 3.5 11.9 - - + -
127A VAL* 3.9 34.1 - - + -
130A GLU* 4.5 3.4 - - - +
154A LYS* 3.3 4.9 - - - -
155A LEU* 2.8 47.4 + - + +
157A PHE* 4.2 15.9 - - + -
1366A GOL 4.0 20.0 - - - +
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Residues in contact with GLU 114 (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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93A PHE 4.3 4.2 + - - -
112A ILE* 4.3 0.4 - - - +
113A LEU* 1.3 72.0 - - - +
115A LYS* 1.3 64.1 + - - +
116A ARG* 3.9 18.5 - - + +
117A HIS* 3.3 28.3 + - + +
118A ILE* 3.2 24.4 + - - +
120A LYS* 5.2 3.3 + - - -
153A GLU* 3.6 16.7 - - + +
154A LYS* 4.3 11.4 - - + +
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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