Contacts of the strand formed by residues 154 - 162 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LYS* 3.3 53.8 + - + +
141A LEU* 3.7 17.9 - - + -
142A LEU 3.0 7.6 - - - +
143A ASN* 4.2 23.3 - - + +
152A ASP* 5.3 7.2 - - - -
153A ARG* 1.3 73.2 - - - +
155A ARG* 1.3 72.4 + - - +
237A THR* 4.9 0.6 + - - -
10F C49 5.1 0.4 + - - -
15M C 5.2 9.3 + - - -
16M T 4.7 12.7 + - - -
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Residues in contact with ARG 155 (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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109A GLU* 3.7 14.8 + - + +
110A ASN 3.1 17.0 - - - +
111A VAL* 3.5 13.7 - - - +
112A LYS 4.4 1.3 - - - +
140A ILE 3.6 0.7 - - - +
141A LEU* 3.3 3.6 - - - +
142A LEU* 2.7 38.1 + - - +
153A ARG* 3.2 49.8 + - + +
154A LYS* 1.3 88.6 + - - +
156A VAL* 1.3 64.1 + - - +
157A PHE* 4.0 23.2 - - + -
237A THR* 3.5 6.3 - - - +
308A VAL* 5.7 0.7 - - + -
309A PRO* 5.8 1.1 - - + -
312A LEU* 5.2 5.4 - - + -
10F C49 2.6 73.2 + - - -
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Residues in contact with VAL 156 (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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108A ALA 3.7 0.8 - - - +
109A GLU* 3.3 6.9 - - - +
110A ASN* 3.0 48.3 + - + +
111A VAL 3.4 17.9 - - - +
112A LYS* 4.9 1.3 - - - -
115A MET* 3.4 46.0 - - + -
139A ILE* 4.8 8.5 - - + -
140A ILE 3.1 9.9 - - - +
141A LEU* 4.1 14.8 - - + -
155A ARG* 1.3 74.4 - - - +
157A PHE* 1.3 66.5 + - - +
158A TYR* 4.2 7.6 - - + -
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Residues in contact with PHE 157 (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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13A LEU* 5.3 1.3 - - + -
107A LEU* 3.9 33.7 - - + -
108A ALA 3.6 2.2 - - - -
109A GLU* 3.4 23.1 - - + -
138A HIS 3.1 8.1 - - - +
139A ILE* 3.4 1.6 - - - -
140A ILE* 2.9 39.3 + - + +
142A LEU* 3.7 29.8 - - + -
155A ARG* 4.0 22.7 - - + -
156A VAL* 1.3 78.6 - - - +
158A TYR* 1.3 62.7 + - - +
159A ILE* 3.0 9.2 + - + +
308A VAL* 4.6 12.3 - - + -
312A LEU* 4.0 16.6 - - + -
313A ALA* 6.3 0.2 - - - -
316A ILE* 3.1 35.2 - - + -
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Residues in contact with TYR 158 (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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91A PHE* 4.1 16.4 - + - -
106A PHE* 2.8 29.6 - - + +
108A ALA* 3.0 36.5 + - + +
110A ASN* 4.8 2.2 - - + -
114A MET* 3.0 34.3 - - + +
115A MET* 2.8 30.9 - - + +
123A VAL* 3.8 10.6 - - + +
126A PHE* 5.5 1.3 - + + -
127A ILE* 4.3 17.9 - - + -
130A PHE* 3.8 30.3 - + + -
137A VAL* 4.6 3.8 - - + -
138A HIS 3.3 5.8 - - - -
139A ILE* 4.1 27.6 - - + -
156A VAL* 4.5 9.0 - - + -
157A PHE* 1.3 70.4 - - - +
159A ILE* 1.3 60.2 + - - +
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Residues in contact with ILE 159 (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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106A PHE* 3.3 8.1 - - - +
107A LEU* 3.7 18.2 - - + -
137A VAL* 3.3 1.4 - - - -
138A HIS* 2.5 52.6 + - + +
140A ILE* 3.7 11.4 - - + -
157A PHE* 3.0 7.6 + - + +
158A TYR* 1.3 73.7 - - - +
160A GLY* 1.3 60.1 + - - +
161A PHE* 3.5 26.2 - - + -
169A TYR* 2.9 37.0 - - + +
316A ILE* 3.5 22.2 - - + -
320A ILE* 3.8 19.3 - - + -
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Residues in contact with GLY 160 (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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105A PHE* 3.1 6.8 - - - +
106A PHE* 2.9 54.2 + - - -
135A TYR* 3.8 6.1 - - - -
136A ASP 3.2 9.9 - - - -
137A VAL* 4.2 1.1 - - - -
158A TYR 3.5 1.2 + - - -
159A ILE* 1.3 76.5 - - - +
161A PHE* 1.3 64.8 + - - -
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Residues in contact with PHE 161 (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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104A ILE* 3.5 6.5 - - + +
105A PHE* 3.9 20.9 - - + -
135A TYR* 2.9 9.5 - - - -
136A ASP* 2.8 41.7 + - + +
138A HIS* 3.8 17.7 - + - -
159A ILE* 3.5 23.8 - - + -
160A GLY* 1.3 75.6 - - - -
162A ARG* 1.3 64.5 + - - +
165A LEU* 5.8 0.2 - - + -
167A ILE* 3.7 43.3 - - + +
169A TYR* 3.7 37.0 - + + -
320A ILE* 3.9 23.3 - - + -
323A ALA* 4.7 0.2 - - + -
324A LEU* 4.1 15.5 - - + -
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Residues in contact with ARG 162 (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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102A LYS* 3.7 34.1 + - - +
103A PRO 3.8 8.3 - - - +
104A ILE* 3.1 37.4 + - - +
134A GLY 3.2 8.5 - - - +
135A TYR* 3.9 8.9 + - + -
136A ASP* 4.6 0.9 - - - +
161A PHE* 1.3 74.9 - - - +
163A LYS* 1.3 65.8 + - - +
164A GLU* 3.2 39.6 + - + +
165A LEU* 2.7 38.1 + - + +
166A ASN 3.5 2.3 + - - -
167A ILE 4.8 0.2 + - - -
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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