Contacts of the strand formed by residues 110 - 117 (chain B) in PDB entry 3HIG
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 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B PHE* 2.8 38.6 + - - +
106B GLN* 3.6 6.2 - - - +
108B HIS 3.5 3.2 + - - +
109B PRO* 1.3 75.9 - - - +
111B VAL* 1.3 58.3 + - - +
112B THR* 2.7 23.7 + - - -
137B SER* 3.7 17.5 - - - +
138B TRP* 3.4 13.5 - - - -
1F NAG 1.4 62.3 + - + +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.4 32.1 - - + -
101B ILE 3.4 8.1 - - - +
102B PHE* 3.7 13.9 - - + -
110B ASN* 1.3 81.7 - - - +
112B THR* 1.3 64.3 + - - +
137B SER* 2.8 28.8 + - - +
138B TRP* 4.2 5.8 - - + -
141B ARG* 3.6 31.2 - - + -
638B TYR* 3.5 24.9 - - + +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ILE 3.0 31.7 + - - +
103B PHE* 4.0 14.2 - - - -
110B ASN* 2.7 23.4 + - - -
111B VAL* 1.3 73.6 + - - +
113B GLU* 1.3 71.6 + - - +
114B PHE* 3.7 27.8 - - + -
127B ALA* 4.4 10.5 - - + -
128B LEU 5.1 4.0 - - - +
1F NAG 3.6 20.5 + - - +
2F NAG 5.6 1.1 - - - +
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ARG* 2.7 50.0 + - + +
99B ALA 3.4 6.3 - - - +
100B VAL* 3.6 9.2 - - + -
111B VAL* 5.1 0.2 - - + -
112B THR* 1.3 79.1 - - - +
114B PHE* 1.3 58.5 + - - +
127B ALA* 3.4 4.2 - - - -
128B LEU* 2.7 53.0 + - + +
129B SER* 6.4 0.4 - - - -
638B TYR* 2.5 39.2 + - + +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA 3.4 3.1 - - - +
98B ARG* 3.4 3.8 - - - -
99B ALA* 2.8 43.6 + - + +
101B ILE* 3.8 16.6 - - + -
103B PHE* 3.9 11.2 - + - -
112B THR* 3.7 31.0 - - + -
113B GLU* 1.3 75.5 - - - +
115B ALA* 1.3 59.9 + - - +
116B VAL* 3.7 9.5 + - + -
125B MET* 3.5 53.6 - - + -
126B ARG 3.2 4.7 - - - +
127B ALA* 3.6 31.6 - - + -
128B LEU* 3.8 6.7 - - - +
2F NAG 3.7 29.2 - - + -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.8 23.8 - - + -
96B GLU* 4.0 18.8 - - - +
97B ALA 3.3 6.1 - - - -
114B PHE* 1.3 70.3 - - - +
116B VAL* 1.3 59.4 + - - +
117B GLY 4.2 0.2 - - - -
124B TYR* 3.8 6.9 - - + -
125B MET* 3.4 3.3 - - - -
126B ARG* 2.7 47.9 + - + +
128B LEU* 3.8 12.5 - - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 4.0 23.1 - - + -
47B PHE* 3.7 28.5 - - + -
48B LEU* 4.1 17.0 - - + -
96B GLU* 3.4 2.2 - - - -
97B ALA* 2.7 43.2 + - + +
99B ALA* 3.9 26.7 - - + -
114B PHE* 4.3 9.4 - - + -
115B ALA* 1.3 76.8 - - - +
117B GLY* 1.3 61.1 + - - +
119B LEU* 4.5 3.5 - - - +
122B PRO* 4.0 10.3 - - + -
124B TYR* 3.5 9.2 - - - +
125B MET* 4.5 2.7 - - + -
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ARG 4.4 2.9 - - - -
96B GLU* 4.6 0.4 - - - -
116B VAL* 1.3 78.7 - - - +
118B PRO* 1.3 72.5 - - - +
119B LEU* 4.5 0.7 - - - -
122B PRO* 3.6 4.7 - - - -
123B CYS 2.7 25.1 + - - -
124B TYR* 2.9 34.8 + - - -
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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