Contacts of the strand formed by residues 154 - 162 (chain B) in PDB entry 1DCT
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 LYS 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS* 3.4 50.4 + - + +
141B LEU* 4.5 9.6 - - + -
142B LEU 3.2 7.0 - - - +
143B ASN* 4.1 27.1 - - + +
152B ASP* 5.2 8.7 - - + -
153B ARG* 1.3 75.4 - - - +
155B ARG* 1.3 77.6 + - - +
237B THR* 5.1 1.0 + - - -
9G G 6.4 0.2 - - - -
10G C49 4.9 0.6 + - - -
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Residues in contact with ARG 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLU* 3.4 13.7 + - - +
110B ASN 3.3 17.7 - - - +
111B VAL* 3.6 11.9 - - - +
112B LYS 4.5 1.3 - - - +
141B LEU* 4.0 1.5 - - - +
142B LEU 2.7 39.9 + - - +
153B ARG* 3.1 33.5 + - + +
154B LYS* 1.3 89.4 + - - +
156B VAL* 1.3 60.9 + - - +
157B PHE* 2.9 29.8 - - + -
237B THR* 3.1 27.5 - - - +
308B VAL* 6.2 0.4 - - + -
309B PRO* 6.0 0.9 - - + -
312B LEU* 5.1 5.2 - - + -
10G C49 2.5 70.1 + - - -
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 4.0 0.4 - - - +
109B GLU* 3.7 0.7 - - - -
110B ASN* 3.2 44.0 + - + +
111B VAL 3.6 17.3 - - - +
112B LYS* 4.8 1.3 - - - -
114B MET* 4.8 0.2 - - - -
115B MET* 3.5 40.4 - - + -
139B ILE* 4.8 7.4 - - + -
140B ILE 3.1 9.9 - - - +
141B LEU* 3.8 26.2 - - + -
155B ARG* 1.3 72.6 - - - +
157B PHE* 1.3 71.8 + - - +
158B TYR* 4.8 7.4 - - + -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 5.8 1.8 - - + -
107B LEU* 4.2 18.6 - - + -
108B ALA 3.6 3.4 - - - +
109B GLU* 3.8 21.1 - - + -
138B HIS 3.2 9.0 - - - +
139B ILE* 3.4 2.2 - - - -
140B ILE* 2.9 38.4 + - + +
142B LEU* 4.0 11.9 - - + -
155B ARG* 2.9 42.2 - - + -
156B VAL* 1.3 75.9 - - - +
158B TYR* 1.3 62.1 - - - +
159B ILE* 3.1 26.3 + - + +
308B VAL* 4.9 9.2 - - + -
312B LEU* 4.2 15.7 - - + -
316B ILE* 3.1 34.1 - - + -
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Residues in contact with TYR 158 (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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91B PHE* 4.0 17.0 - + - -
106B PHE* 3.5 17.9 - - + +
107B LEU* 3.2 3.1 - - - -
108B ALA* 2.8 53.9 + - + +
110B ASN* 4.7 6.5 - - + -
114B MET* 2.7 49.3 - - + +
115B MET* 4.1 6.7 - - + +
123B VAL* 3.5 29.5 - - + +
126B PHE* 5.0 1.3 - + + -
127B ILE* 4.2 16.6 - - + -
130B PHE* 4.1 21.3 - + + -
137B VAL* 4.8 3.6 - - + -
138B HIS 3.6 4.9 - - - -
139B ILE* 4.5 17.5 - - + +
156B VAL* 4.8 8.1 - - + -
157B PHE* 1.3 72.5 - - - +
159B ILE* 1.3 60.7 + - - +
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Residues in contact with ILE 159 (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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105B PHE* 5.6 0.4 - - + -
106B PHE* 3.1 8.5 - - - +
107B LEU* 3.3 27.4 - - + -
137B VAL* 3.7 0.9 - - - -
138B HIS* 2.6 51.0 + - + +
140B ILE* 3.8 13.9 - - + -
157B PHE* 3.6 14.6 - - + +
158B TYR* 1.3 75.3 - - - +
160B GLY* 1.3 56.9 + - - +
161B PHE* 4.1 15.5 - - + -
169B TYR* 3.4 29.2 - - + +
316B ILE* 3.6 11.9 - - + -
320B ILE* 3.9 26.7 - - + -
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Residues in contact with GLY 160 (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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105B PHE* 2.9 7.1 - - - +
106B PHE* 2.8 59.2 + - - -
135B TYR* 4.4 0.9 - - - -
136B ASP 3.0 15.0 - - - -
138B HIS* 4.0 3.1 - - - -
159B ILE* 1.3 76.7 - - - +
161B PHE* 1.3 65.1 + - - -
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Residues in contact with PHE 161 (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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104B ILE 3.3 7.9 - - - +
105B PHE* 3.5 22.0 - - + -
135B TYR* 3.2 6.5 - - - -
136B ASP* 2.8 31.5 + - - +
138B HIS* 3.6 20.2 - + - -
159B ILE* 4.1 10.5 - - + -
160B GLY* 1.3 73.7 - - - -
162B ARG* 1.3 68.1 + - - +
165B LEU* 4.2 1.3 - - + -
167B ILE* 3.6 38.8 - - + -
169B TYR* 3.5 42.8 - + + -
320B ILE* 4.0 19.7 - - + -
323B ALA* 4.4 0.9 - - + -
324B LEU* 3.9 29.6 - - + -
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 2.6 35.9 + - - +
103B PRO* 3.7 8.2 - - - +
104B ILE* 3.0 38.8 + - - +
134B GLY 3.1 10.1 - - - +
135B TYR* 3.3 19.8 + - + -
136B ASP* 4.2 1.4 - - - +
161B PHE* 1.3 71.5 - - - +
163B LYS* 1.3 68.3 + - - +
164B GLU* 3.0 37.3 + - + -
165B LEU* 3.0 32.1 + - + +
166B ASN 3.8 2.3 + - - -
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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