Contacts of the strand formed by residues 174 - 181 (chain B) in PDB entry 3R9X
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 SER 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B MET* 4.1 13.3 - - - +
128B VAL 3.1 19.5 + - - -
129B GLN* 3.8 7.3 - - - +
130B LYS* 3.7 3.9 - - - +
160B THR* 3.7 6.6 - - - +
161B VAL* 2.7 34.1 + - - +
166B PHE* 3.9 29.2 - - - -
172B VAL 3.8 1.1 + - - -
173B GLN* 1.3 74.6 - - - +
175B ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE 3.9 0.2 - - - +
127B MET* 3.3 4.2 - - - +
128B VAL* 2.7 34.8 + - - +
130B LYS* 4.4 7.0 - - - -
133B ALA* 4.4 13.9 - - + -
157B TYR* 3.5 35.9 - - + +
159B MET 3.3 8.3 - - - +
161B VAL* 3.8 4.7 - - - -
174B SER* 1.3 78.4 - - - +
176B VAL* 1.3 64.8 + - - +
177B ILE 4.0 0.4 + - - -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 5.2 2.9 - - + -
21B LYS* 6.1 2.5 - - + -
22B ILE* 4.0 25.8 - - + -
25B GLU* 5.7 1.6 - - + -
125B VAL* 4.0 22.2 - - + -
126B PHE 3.3 10.5 - - - +
127B MET* 4.6 5.8 - - + -
157B TYR* 4.1 0.7 - - - -
158B VAL* 2.9 42.2 + - + -
159B MET* 2.9 38.9 + - + +
161B VAL* 3.9 11.4 - - + -
175B ALA* 1.3 78.3 - - - +
177B ILE* 1.3 66.8 + - - +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 5.1 2.5 - - + -
124B ALA 4.1 0.3 - - - +
125B VAL* 3.5 5.4 - - - +
126B PHE* 2.7 55.2 + - + +
128B VAL* 3.8 23.6 - - + -
133B ALA* 3.6 26.5 - - + +
136B LEU* 3.6 31.4 - - + -
137B GLN* 5.8 0.7 - - + -
155B VAL* 4.7 13.0 - - + -
156B ASN 3.4 9.4 - - - +
157B TYR* 4.5 11.4 - - + -
158B VAL* 4.5 1.8 - - - -
175B ALA 4.0 0.4 + - - -
176B VAL* 1.3 80.8 - - - +
178B LYS* 1.3 60.7 + - - +
179B LEU* 4.5 12.3 - - + -
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Residues in contact with LYS 178 (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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25B GLU* 3.7 41.8 + - + +
27B ASN* 5.2 7.5 - - - +
123B LEU* 3.6 25.3 - - + +
124B ALA 3.5 3.6 - - - +
125B VAL* 4.2 11.7 - - + +
154B ASP 3.5 1.7 - - - +
156B ASN* 2.8 55.8 + - + +
158B VAL* 3.7 13.7 - - + -
177B ILE* 1.3 74.8 - - - +
179B LEU* 1.3 64.0 + - - +
180B VAL* 4.0 15.6 - - + +
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Residues in contact with LEU 179 (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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111B ILE* 4.9 13.0 - - + -
114B THR* 5.8 4.3 - - + -
115B VAL* 5.7 2.7 - - + -
123B LEU* 3.0 9.4 - - - +
124B ALA* 2.7 44.3 + - + +
126B PHE* 4.3 27.4 - - + -
136B LEU* 5.5 2.7 - - + -
149B VAL* 4.4 14.1 - - + -
153B TYR* 3.9 27.6 - - + -
154B ASP 3.6 1.8 - - - -
155B VAL* 4.2 27.6 - - + -
177B ILE* 4.5 13.9 - - + -
178B LYS* 1.3 81.8 - - - +
180B VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 180 (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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122B PRO 4.0 7.6 - - - +
123B LEU* 4.0 21.1 - - + -
153B TYR* 3.5 4.7 - - - -
154B ASP* 2.9 39.2 + - + +
156B ASN* 3.3 28.5 - - - +
178B LYS* 4.1 15.3 - - + +
179B LEU* 1.3 76.1 - - - +
181B LYS* 1.3 73.5 + - - +
182B ASN* 3.0 0.9 + - - +
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Residues in contact with LYS 181 (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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118B LYS* 3.0 36.2 - - - +
119B ASP* 4.4 12.3 + - - +
121B VAL 4.4 0.4 - - - +
122B PRO* 3.1 42.1 + - + +
152B PHE* 4.2 6.5 - - + +
153B TYR* 3.5 15.8 - - + -
180B VAL* 1.3 75.2 - - - +
182B ASN* 1.3 63.1 + - - +
183B GLU* 3.1 32.1 + - + +
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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