Contacts of the strand formed by residues 146 - 152 (chain C) in PDB entry 1H9D
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 PHE 146 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ALA* 4.0 12.6 - - + -
108C GLY* 3.5 24.2 - - - +
109C ASN* 4.0 3.1 - - - -
112C ASN* 3.9 12.8 - - + -
115C ALA* 3.2 30.3 - - + -
136C PHE* 4.2 13.5 - + - -
138C GLY 3.3 17.0 - - - -
139C ARG 3.1 30.7 - - - -
140C SER* 3.5 21.5 - - - -
145C SER* 1.3 74.2 - - - +
147C THR* 1.3 63.0 + - - +
148C LEU* 4.0 1.8 - - + -
164C ARG 3.4 1.4 + - - -
165C ALA* 3.0 26.5 + - - +
166C ILE* 2.7 22.9 + - + +
168C ILE* 3.9 19.7 - - + -
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Residues in contact with THR 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ALA* 3.4 2.9 - - - -
108C GLY 2.8 32.5 + - - -
109C ASN* 5.2 4.1 - - - +
145C SER 4.0 2.3 + - - -
146C PHE* 1.3 75.3 - - - +
148C LEU* 1.3 71.5 + - - +
149C THR* 4.0 3.8 + - - +
161C THR* 4.5 5.4 - - + -
162C TYR 3.5 9.4 - - - +
163C HIS* 3.4 45.4 - - + +
164C ARG* 3.8 7.3 + - - +
60D THR 5.7 1.6 - - - -
61D GLY 4.9 3.8 - - - +
62D THR* 5.2 11.4 - - + +
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Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 3.9 24.7 - - + -
89C PHE* 4.1 15.9 - - + -
105C VAL* 4.3 15.0 - - + -
106C MET 3.3 4.3 - - - +
107C ALA* 3.7 15.5 - - + -
134C LEU* 6.0 0.4 - - + -
136C PHE* 3.6 30.5 - - + -
146C PHE* 4.6 5.6 - - + -
147C THR* 1.3 77.0 - - - +
149C THR* 1.3 63.4 + - - +
150C ILE* 4.1 5.8 - - + -
161C THR* 3.0 30.3 - - - +
162C TYR* 2.8 34.4 + - + +
165C ALA* 3.9 13.2 - - + -
166C ILE* 4.8 1.1 - - + -
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Residues in contact with THR 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C THR 3.6 1.4 - - - +
105C VAL* 3.4 4.5 - - - -
106C MET* 2.7 43.4 + - + +
147C THR* 4.9 3.3 + - - +
148C LEU* 1.3 74.0 + - - +
150C ILE* 1.3 61.2 + - - +
151C THR* 3.8 11.9 + - - +
159C VAL* 3.6 26.0 - - + -
160C ALA 3.8 2.2 - - - -
161C THR* 4.1 10.1 - - + +
62D THR* 4.3 4.5 - - - +
63D ASN* 2.8 39.6 + - - +
64D LEU* 4.3 2.9 - - + -
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C THR* 4.3 12.3 - - + -
70C PHE* 5.8 1.6 - - + -
72C CYS* 4.1 30.5 - - + -
89C PHE* 4.2 8.3 - - + -
91C VAL* 3.8 31.4 - - + -
103C VAL* 3.9 14.6 - - + -
104C THR 3.4 4.5 - - - +
105C VAL* 4.4 14.8 - - + -
148C LEU* 4.9 7.0 - - + -
149C THR* 1.3 74.8 - - - +
151C THR* 1.3 60.9 + - - +
152C VAL* 4.5 5.5 - - + +
158C GLN 3.9 0.9 - - - +
159C VAL* 3.3 2.9 - - - +
160C ALA* 2.7 54.2 + - + +
162C TYR* 5.0 9.4 - - + -
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Residues in contact with THR 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C VAL* 3.2 7.3 - - - +
104C THR* 3.0 35.6 + - - -
106C MET* 4.1 12.6 - - - +
149C THR* 3.8 17.0 + - - +
150C ILE* 1.3 73.9 - - - +
152C VAL* 1.3 64.1 + - - +
153C PHE* 3.7 36.6 - - + -
157C PRO* 4.1 12.3 - - + -
158C GLN 3.5 3.6 - - - +
159C VAL* 4.0 19.9 - - + +
65D SER* 4.5 9.2 + - - +
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PHE* 3.4 41.3 - - + -
91C VAL* 4.7 0.4 - - + -
97C VAL* 4.1 16.8 - - + -
101C THR* 3.7 19.1 - - + -
102C LEU 3.8 2.9 - - - -
103C VAL* 4.0 23.1 - - + -
124C MET* 4.6 3.8 - - + -
150C ILE* 4.5 7.9 - - + +
151C THR* 1.3 77.0 - - - +
153C PHE* 1.3 59.5 + - - +
154C THR* 3.1 13.7 + - + +
157C PRO* 3.3 1.4 - - - +
158C GLN* 2.7 43.1 + - + +
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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