Contacts of the strand formed by residues 166 - 173 (chain A) in PDB entry 3HN3
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 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG 3.7 1.2 - - - +
104A GLU* 3.2 2.6 - - - -
105A VAL* 2.6 45.6 + - + +
107A LEU* 3.8 27.5 - - + +
134A VAL* 3.3 32.3 - - + -
135A ASN* 3.7 13.7 - - - +
153A ILE* 3.9 17.3 - - + -
157A VAL* 4.2 18.8 - - + -
164A SER 3.6 3.4 + - - -
165A ARG* 1.3 70.2 - - - +
167A ARG* 1.3 59.2 + - - +
168A ILE* 4.0 19.3 - - + -
220A LEU* 4.0 18.4 - - + -
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Residues in contact with ARG 167 (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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64A TYR 2.9 29.5 + - - -
65A ARG 3.4 19.0 + - - -
66A ARG* 3.3 14.8 + - - +
67A PRO* 3.9 14.6 - - - +
102A GLU* 2.9 46.8 + - + -
103A ARG 3.5 3.4 - - - -
104A GLU* 3.6 28.3 - - + +
133A TRP 3.7 0.7 - - - +
134A VAL* 3.5 5.4 - - - +
135A ASN* 2.9 48.5 + - - +
136A GLY* 3.7 17.4 + - - +
165A ARG 3.5 2.6 + - - +
166A LEU* 1.3 71.2 - - - +
168A ILE* 1.3 60.7 + - - +
169A THR* 3.2 10.4 + - - +
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Residues in contact with ILE 168 (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* 3.7 29.2 - - + -
45A TRP* 4.0 13.3 - - + -
101A TYR 4.0 0.2 - - - +
102A GLU* 3.2 5.8 - - - +
103A ARG* 2.9 34.5 + - + +
105A VAL* 4.0 17.3 - - + -
121A LEU* 3.8 34.5 - - + -
132A VAL* 4.4 3.4 - - + -
133A TRP 3.6 3.6 - - - +
134A VAL* 4.7 5.6 - - + -
166A LEU* 4.0 21.3 - - + -
167A ARG* 1.3 74.2 - - - +
169A THR* 1.3 62.6 + - - +
170A ILE* 4.0 26.0 - - + -
220A LEU* 4.9 0.7 - - + -
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Residues in contact with THR 169 (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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64A TYR* 4.1 10.8 - - + -
68A LEU* 5.4 4.9 - - + -
100A TRP* 4.1 20.6 - - + -
101A TYR 3.3 10.1 - - - +
102A GLU* 2.7 26.5 + - + +
132A VAL* 3.3 3.1 - - - +
133A TRP* 2.8 63.5 + - + +
136A GLY 5.6 0.2 + - - -
167A ARG* 3.2 15.0 + - - +
168A ILE* 1.3 72.5 - - - +
170A ILE* 1.3 67.8 + - - +
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Residues in contact with ILE 170 (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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45A TRP* 4.0 24.9 - - + -
99A VAL 3.8 1.0 - - - +
100A TRP* 3.5 1.9 - - - -
101A TYR* 2.8 47.8 + - + +
123A ILE* 3.7 29.6 - - + -
130A ALA* 4.6 6.3 - - + -
131A ILE 3.3 10.3 - - - +
132A VAL* 4.0 15.7 - - + -
133A TRP* 4.5 1.1 - - - -
149A PHE* 5.7 2.7 - - + -
168A ILE* 4.0 13.0 - - + -
169A THR* 1.3 80.6 - - - +
171A ALA* 1.3 62.2 + - - +
172A ILE* 4.0 22.8 + - + -
214A LEU* 4.1 16.8 - - + -
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Residues in contact with ALA 171 (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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59A PHE* 4.3 0.4 - - + -
98A TRP* 3.6 23.0 - - + -
99A VAL 3.2 7.9 - - - +
100A TRP* 4.0 20.4 - - + +
130A ALA* 3.2 5.0 - - - -
131A ILE* 2.9 31.8 + - + +
133A TRP* 3.6 27.2 - - + -
170A ILE* 1.3 72.9 - - - +
172A ILE* 1.3 59.0 + - - +
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Residues in contact with ILE 172 (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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97A GLY 3.6 1.7 - - - +
98A TRP* 3.4 4.0 - - - -
99A VAL* 2.9 43.4 + - + +
101A TYR* 3.8 20.4 - - + -
126A ALA* 4.4 4.5 - - + -
127A HIS* 3.5 32.8 - - + +
129A TYR 3.3 6.3 - - - +
130A ALA* 4.4 7.0 - - + -
170A ILE* 4.0 12.3 - - + -
171A ALA* 1.3 78.3 - - - +
173A ASN* 1.3 62.5 + - - +
174A ASN* 4.1 1.3 + - + +
212A ALA* 5.2 3.1 - - + -
213A GLY* 3.9 18.4 - - - +
214A LEU* 3.6 36.6 - - + -
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Residues in contact with ASN 173 (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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97A GLY 3.3 6.7 + - - -
98A TRP* 3.1 32.8 - - + +
127A HIS* 3.5 2.9 - - - +
128A SER* 3.1 24.9 + - - -
129A TYR* 2.7 15.0 + - + +
172A ILE* 1.3 73.8 - - - +
174A ASN* 1.3 59.6 + - - +
175A THR* 2.9 34.5 + - - -
1C NAG 1.4 67.8 + - - +
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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