Contacts of the strand formed by residues 168 - 177 (chain A) in PDB entry 6O4P
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 GLN 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LYS* 2.9 56.9 + - + +
130A THR 3.9 13.3 + - - +
167A SER* 1.3 81.7 + - - +
169A TYR* 1.3 67.1 + - - +
187A ASP* 4.0 12.6 - - + +
188A VAL 3.6 14.8 - - - +
189A SER* 4.3 14.5 - - - +
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Residues in contact with TYR 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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106A PHE* 4.3 19.5 - + + -
126A TYR* 3.5 34.3 - + + -
127A ARG 3.6 4.0 - - - -
128A LYS* 3.2 38.7 - - + -
129A LYS* 4.5 2.2 - - - -
160A VAL* 4.7 0.9 - - + -
163A ALA* 3.2 16.8 - - + -
164A GLU* 2.6 46.9 + - - +
167A SER* 3.7 10.5 - - - -
168A GLN* 1.3 81.0 - - - +
170A ARG* 1.3 57.1 - - - +
171A ILE* 3.9 17.3 - - + -
187A ASP* 3.3 5.7 - - - +
188A VAL* 2.5 50.3 + - + +
190A LEU* 5.1 7.0 - - + -
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Residues in contact with ARG 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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126A TYR* 3.4 18.5 - - - -
127A ARG* 3.4 27.9 + - + +
129A LYS* 3.3 23.3 - - + +
169A TYR* 1.3 74.3 - - - +
171A ILE* 1.3 63.6 + - - +
172A ASN* 3.7 2.6 + - - +
185A LEU* 3.8 48.5 - - + +
186A LEU 3.5 5.6 - - - +
187A ASP* 2.7 40.1 + - - +
1C NAG 5.7 0.2 - - - -
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Residues in contact with ILE 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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96A VAL* 4.0 17.5 - - + -
98A CYS* 4.5 1.1 - - - -
106A PHE* 3.9 20.2 - - + -
108A CYS* 3.7 22.4 - - + -
124A THR* 6.5 0.2 - - - -
125A SER 3.6 5.4 - - - +
126A TYR* 4.4 11.4 - - + -
148A CYS* 5.4 6.1 - - - -
158A CYS* 5.5 3.4 - - - -
169A TYR* 3.9 12.6 - - + -
170A ARG* 1.3 74.5 - - - +
172A ASN* 1.3 60.0 + - - +
173A VAL* 3.9 24.2 - - + -
184A ARG 3.2 7.5 - - - +
185A LEU* 3.3 2.8 - - - -
186A LEU* 2.9 37.5 + - + +
188A VAL* 3.9 27.6 - - + -
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Residues in contact with ASN 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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123A LEU 3.3 6.1 - - - +
124A THR* 3.4 1.4 - - - -
125A SER* 2.7 48.9 + - - +
126A TYR* 5.5 0.2 - - - -
170A ARG 3.7 2.4 + - - +
171A ILE* 1.3 72.0 - - - +
173A VAL* 1.3 62.4 + - - +
174A THR* 2.8 15.1 + - - -
183A THR* 3.2 12.1 - - - +
184A ARG 3.7 3.1 - - - -
185A LEU* 4.1 9.6 - - + -
1C NAG 1.4 69.3 + - + +
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Residues in contact with VAL 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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94A PRO* 3.7 26.2 - - + +
96A VAL* 3.6 26.7 - - + -
108A CYS* 5.8 0.2 - - + -
110A TRP* 3.8 41.1 - - + -
122A TYR* 4.0 11.2 - - + -
123A LEU 3.4 3.8 - - - +
124A THR* 4.4 9.2 - - + -
158A CYS* 5.6 2.5 - - - -
171A ILE* 3.9 15.9 - - + -
172A ASN* 1.3 75.8 + - - +
174A THR* 1.3 61.5 + - - +
184A ARG 3.0 28.2 + - - -
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Residues in contact with THR 174 (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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122A TYR* 3.3 9.3 - - - -
123A LEU* 2.9 38.2 + - + +
172A ASN* 2.8 22.7 + - - -
173A VAL* 1.3 70.6 - - - +
175A GLU* 1.3 62.7 + - - +
176A VAL* 3.7 22.7 + - + -
181A ALA* 3.9 14.6 - - + -
182A SER 3.2 10.3 - - - +
183A THR* 3.2 16.4 + - - +
1C NAG 3.3 25.9 + - - -
2C NAG 5.1 1.3 - - - +
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Residues in contact with GLU 175 (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 PRO* 3.3 29.0 - - + +
92A ALA 3.0 22.5 + - - +
94A PRO* 3.9 14.0 - - + +
112A PRO* 3.5 29.2 - - - +
113A SER 4.5 0.3 + - - -
114A GLN 4.4 5.0 - - - +
116A SER* 4.1 12.8 + - - -
120A THR* 3.5 21.8 - - + +
121A ARG 3.8 4.0 - - - -
122A TYR* 3.7 21.9 + - + -
173A VAL 4.0 1.6 + - - -
174A THR* 1.3 71.0 - - - +
176A VAL* 1.3 58.5 + - - +
177A ASN* 5.0 0.2 + - - -
181A ALA* 3.4 0.2 - - - -
182A SER 2.8 33.2 + - - +
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Residues in contact with VAL 176 (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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119A PRO 4.1 0.2 - - - +
120A THR* 3.3 6.8 - - - +
121A ARG* 3.0 55.7 + - + +
123A LEU* 3.7 24.5 - - + -
174A THR* 3.7 13.0 - - + +
175A GLU* 1.3 76.7 - - - +
177A ASN* 1.3 60.4 + - - +
180A GLY 3.5 5.6 - - - +
181A ALA* 3.6 23.8 - - + -
2C NAG 4.3 8.3 - - + +
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Residues in contact with ASN 177 (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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89A TYR 2.8 27.1 + - - -
91A PRO* 3.1 35.5 - - - +
116A SER* 3.5 16.2 + - - -
118A LEU* 4.2 8.8 - - + +
119A PRO 3.7 9.9 - - - +
120A THR* 4.0 9.4 - - + +
175A GLU 4.3 0.2 - - - -
176A VAL* 1.3 74.7 - - - +
178A PRO* 1.3 66.5 - - + +
179A LEU* 2.6 27.2 + - - -
180A GLY 3.0 13.5 + - - +
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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