Contacts of the strand formed by residues 121 - 126 (chain C) in PDB entry 3DH1
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 121 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C THR 4.3 0.2 + - - -
99C VAL* 3.5 35.3 - - + -
100C LEU 3.1 23.0 + - - -
119C ILE* 3.5 6.3 - - - +
120C PRO* 1.3 85.7 - - + +
122C VAL* 1.3 66.6 + - - +
123C VAL* 4.8 3.6 - - + -
153C GLN* 3.4 29.8 - - + +
155C ILE* 4.2 29.6 - - + -
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 3.4 16.2 - - + +
102C VAL* 4.0 26.5 - - + -
106C PRO* 4.6 7.0 - - + -
114C LEU* 4.0 19.7 - - + -
119C ILE* 4.5 4.9 - - + -
121C LEU* 1.3 77.8 - - - +
123C VAL* 1.3 66.2 + - - +
124C TYR* 4.1 13.0 + - + -
152C PHE* 3.4 33.2 - - + -
153C GLN 2.8 11.4 + - - +
154C CYS* 3.2 7.9 - - - +
155C ILE 3.0 22.9 + - - -
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C THR* 4.0 21.1 - - + -
26C MET* 3.6 30.9 - - + +
99C VAL* 4.9 2.0 - - + +
100C LEU 2.8 7.1 + - - +
101C TYR* 3.3 18.2 - - + -
102C VAL* 2.9 24.6 + - - +
121C LEU* 4.2 10.0 - - + -
122C VAL* 1.3 72.0 - - - +
124C TYR* 1.3 65.2 + - - +
155C ILE* 3.6 41.3 - - + +
158C TYR* 4.7 7.6 - - + -
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Residues in contact with TYR 124 (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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26C MET* 3.5 8.2 - - - +
102C VAL* 3.0 28.9 - - + +
105C GLU* 3.7 38.9 - - + +
106C PRO* 4.2 6.7 - - + -
122C VAL* 4.1 15.7 - - + -
123C VAL* 1.3 73.4 - - - +
125C GLY* 1.3 72.1 + - - +
126C CYS 3.7 9.9 - - - -
127C GLN* 3.7 20.6 + - - -
134C CYS* 4.1 11.1 + - + +
154C CYS* 4.0 27.8 - - + -
155C ILE 3.2 8.5 + - - +
156C PRO* 3.3 31.6 - - + +
157C GLY 3.0 19.8 + - - -
158C TYR* 3.3 7.6 + - - +
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Residues in contact with GLY 125 (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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26C MET* 3.8 1.5 - - - +
102C VAL 3.1 9.1 + - - -
103C THR* 3.3 10.1 + - - -
124C TYR* 1.3 79.2 - - - +
126C CYS* 1.3 64.0 + - - -
127C GLN* 5.1 1.4 + - - -
157C GLY* 2.9 26.2 + - - -
158C TYR 3.5 20.6 - - - -
160C ALA* 3.8 7.7 - - - +
163C ALA* 4.6 2.9 - - - -
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Residues in contact with CYS 126 (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 THR 3.2 8.0 + - - -
104C VAL* 3.9 15.7 - - - -
105C GLU 3.0 25.6 + - - -
124C TYR* 3.7 3.8 - - - -
125C GLY* 1.3 75.3 - - - -
127C GLN* 1.3 69.9 + - - +
160C ALA* 3.6 28.9 - - + +
163C ALA* 3.4 22.9 - - - +
164C VAL* 3.7 23.6 - - + +
167C LEU* 4.2 5.8 - - - -
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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