Contacts of the strand formed by residues 112 - 119 (chain A) in PDB entry 1H8F
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 LEU 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLY* 3.2 23.4 - - - -
46A GLN* 3.6 13.5 + - - +
98A LEU* 3.7 27.8 - - + -
101A MET* 3.9 30.9 + - + +
102A ARG* 4.1 13.0 - - + +
110A VAL 4.0 2.0 + - - -
111A ARG* 1.3 71.8 + - - +
113A ARG* 1.3 63.7 + - - +
114A TYR 3.2 22.9 - - - +
115A PHE* 4.2 8.3 - - + -
130A LEU* 3.7 31.2 - - + -
131A VAL 3.9 3.6 - - - +
132A LEU* 3.9 14.8 - - + +
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Residues in contact with ARG 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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44A PRO* 3.6 1.4 - - - +
45A GLY 2.9 18.1 + - - -
75A LEU* 3.7 21.5 - - - +
80A GLU* 2.6 46.3 + - - +
82A VAL* 3.5 24.1 - - - +
111A ARG* 3.3 19.7 + - + +
112A LEU* 1.3 72.9 - - - +
114A TYR* 1.3 93.6 + - + +
131A VAL* 2.8 16.6 + - + +
133A ASP* 2.7 37.6 + - - +
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Residues in contact with TYR 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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42A ALA* 3.5 22.2 - - + -
43A THR 3.4 7.9 - - - +
44A PRO* 4.0 15.9 - - + -
45A GLY 4.2 0.9 - - - +
52A GLN* 3.6 25.0 + - - -
54A VAL* 4.0 36.2 - - + +
75A LEU* 4.7 9.1 - - + +
77A ASP* 5.4 2.9 + - - -
112A LEU* 3.2 10.1 - - - +
113A ARG* 1.3 113.8 + - + +
115A PHE* 1.3 68.2 + - - +
131A VAL* 3.0 41.0 + - + -
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Residues in contact with PHE 115 (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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43A THR* 3.2 65.7 + - + -
44A PRO 3.6 12.1 - - - -
45A GLY 4.8 0.2 - - - -
49A ASP* 5.0 1.3 - - - -
98A LEU* 3.7 31.9 - - + -
102A ARG* 3.7 37.2 - - - -
112A LEU* 4.2 7.6 - - + -
114A TYR* 1.3 81.6 - - - +
116A PHE* 1.3 65.5 + - - +
117A TYR* 4.4 15.5 - + - -
128A LEU* 4.3 8.1 - - + -
129A ASN 3.1 15.3 - - - +
130A LEU* 4.0 15.3 - - + -
131A VAL 4.5 0.4 - - - +
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Residues in contact with PHE 116 (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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40A VAL* 4.0 38.8 - - + -
41A VAL 3.8 21.1 - - - +
42A ALA* 4.0 9.9 - - + -
56A TYR* 4.1 23.1 - + - -
84A ILE* 4.7 4.0 - - + -
115A PHE* 1.3 78.8 - - - +
117A TYR* 1.3 83.9 + - - +
118A SER* 4.4 7.6 - - - -
128A LEU* 3.7 4.2 - - - +
129A ASN* 2.8 67.2 + - + +
131A VAL* 3.7 22.9 - - + -
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Residues in contact with TYR 117 (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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89A GLN* 4.2 10.2 - - + +
91A LYS* 3.5 31.6 + - - -
94A LYS* 5.7 2.8 + - - -
95A ASN* 5.7 1.0 - - - +
98A LEU* 4.0 13.3 - - - +
115A PHE* 4.4 14.7 - + - -
116A PHE* 1.3 88.8 - - - +
118A SER* 1.3 66.2 + - - +
126A VAL* 3.9 18.6 - - + -
127A TYR 3.2 13.5 - - - +
128A LEU* 3.6 34.4 - - + +
129A ASN* 3.9 0.9 - - - -
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Residues in contact with SER 118 (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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40A VAL* 6.4 0.4 - - - -
86A LYS* 3.9 11.8 + - - -
116A PHE* 4.5 8.1 - - - -
117A TYR* 1.3 77.2 - - - +
119A SER* 1.3 68.5 + - - +
126A VAL* 4.9 1.5 - - - +
127A TYR* 3.0 31.0 + - - +
129A ASN* 3.1 23.3 + - - -
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Residues in contact with SER 119 (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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86A LYS* 5.4 1.4 + - - -
118A SER* 1.3 77.2 + - - +
120A GLY* 1.3 63.9 + - - +
124A ASP* 5.3 9.2 - - - -
125A GLU 3.1 13.9 - - - -
126A VAL* 4.4 5.5 - - - +
127A TYR* 4.6 1.1 - - - -
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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