Contacts of the strand formed by residues 83 - 97 (chain B) in PDB entry 5UWS
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 GLU 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA* 6.0 1.0 - - - +
79B MET 4.7 1.3 - - - -
80B GLU* 3.7 21.3 - - - +
81B GLU 3.1 7.8 + - - +
82B ASP* 1.3 84.0 - - + +
84B GLU* 1.3 61.5 + - - +
85B VAL* 5.5 1.6 - - - +
114B LEU* 3.3 33.0 - - + +
115B LYS 3.4 6.5 - - - +
116B ASN* 3.9 25.1 + - + +
117B LYS* 3.7 14.7 + - - +
123B ARG* 2.8 48.7 + - - +
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Residues in contact with GLU 84 (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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83B GLU* 1.3 74.8 - - - +
85B VAL* 1.3 73.2 + - - +
86B LEU* 3.5 17.9 + - + +
114B LEU* 3.2 7.3 - - - -
115B LYS* 2.9 63.4 + - + +
117B LYS* 4.5 13.7 - - + +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU 5.5 1.8 - - - +
84B GLU* 1.3 81.4 - - - +
86B LEU* 1.3 64.0 + - - +
87B TYR 3.9 22.4 - - - +
88B LYS* 4.3 15.3 - - + -
112B LYS* 4.7 15.9 - - + +
113B PHE 3.7 4.0 - - - +
114B LEU* 3.8 19.3 - - + -
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Residues in contact with LEU 86 (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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84B GLU* 3.9 28.0 - - - +
85B VAL* 1.3 75.2 - - - +
87B TYR* 1.3 60.4 + - + +
113B PHE* 2.9 21.5 + - + +
115B LYS* 3.9 25.6 - - + +
122B VAL* 3.6 37.7 - - + -
190B GLU* 4.3 11.7 - - - +
194B ALA* 5.2 4.0 - - + -
197B ILE* 4.2 16.6 - - + -
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Residues in contact with TYR 87 (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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85B VAL* 3.9 5.8 - - - +
86B LEU* 1.3 81.3 - - + +
88B LYS* 1.3 78.2 + - - +
89B VAL* 3.3 39.6 - - + +
111B CYS 5.2 0.7 - - - -
112B LYS* 3.3 3.6 - - - -
113B PHE* 2.9 57.6 + + + -
183B ASN* 3.6 20.8 + - - +
186B LYS* 4.2 13.9 - - + +
187B PHE* 3.7 27.3 + + - -
190B GLU* 3.7 33.2 - - + +
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Residues in contact with LYS 88 (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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85B VAL* 4.3 13.7 - - + -
87B TYR* 1.3 89.3 - - - +
89B VAL* 1.3 65.8 + - - +
110B ASP* 4.4 24.9 + - + +
111B CYS 3.4 4.9 - - - +
112B LYS* 3.9 37.7 - - + +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 3.3 38.4 - - + +
88B LYS* 1.3 76.9 - - - +
90B ARG* 1.3 70.1 + - - +
110B ASP* 4.4 3.6 - - - -
111B CYS* 2.7 47.7 + - + +
178B PHE* 3.7 31.0 - - + -
183B ASN* 4.4 21.8 - - + +
187B PHE* 4.2 3.4 - - + -
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Residues in contact with ARG 90 (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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216A LEU* 3.3 41.0 - - + +
89B VAL* 1.3 85.4 - - - +
91B ALA* 1.3 61.0 + - - +
108B THR* 3.9 8.1 - - - +
109B GLY* 3.4 14.4 - - - +
110B ASP* 3.0 24.2 - - - +
129B ASP* 2.8 36.0 + - - -
178B PHE* 3.9 5.4 - - - +
179B GLY 4.7 1.2 + - - -
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Residues in contact with ALA 91 (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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216A LEU* 3.9 9.3 - - - +
89B VAL 3.7 3.6 + - - +
90B ARG* 1.3 76.0 - - - +
92B LYS* 1.3 61.4 + - - +
108B THR* 3.5 4.5 - - - +
109B GLY 3.0 18.6 + - - -
111B CYS* 4.6 2.2 - - + -
126B MET* 3.1 20.7 - - + +
176B ILE* 3.5 31.4 - - + -
177B ARG 3.1 15.7 - - - +
178B PHE* 3.7 9.9 - - + -
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Residues in contact with LYS 92 (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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29A ARG* 5.8 0.8 - - - +
154A ASN* 5.9 1.8 - - - +
211A ASP* 6.3 0.7 - - - -
214A ASP* 5.5 6.7 - - - -
215A ASP 5.8 0.2 + - - -
216A LEU* 3.8 27.2 - - + +
91B ALA* 1.3 74.1 - - - +
93B LEU* 1.3 63.0 + - - +
94B PHE* 3.6 29.3 - - + -
105B GLU* 3.2 38.3 + - + -
107B GLY 3.7 3.8 - - - +
108B THR* 2.9 35.3 + - - +
126B MET* 4.4 0.2 - - - -
175B ALA 3.7 0.7 - - - +
176B ILE* 3.4 3.2 - - - -
177B ARG* 2.8 47.2 + - + +
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Residues in contact with LEU 93 (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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92B LYS* 1.3 74.2 - - - +
94B PHE* 1.3 60.6 + - - +
105B GLU* 3.6 4.2 - - - +
106B ARG* 2.7 45.0 + - + -
107B GLY 2.9 18.0 + - - +
126B MET* 3.9 18.1 - - + +
135B CYS* 3.0 30.3 - - - +
136B ALA* 3.6 18.4 - - + -
138B HIS* 6.3 0.7 - - + -
158B TYR* 5.6 3.1 - - + +
174B PHE* 4.0 31.0 - - + -
175B ALA 3.5 15.7 - - - +
176B ILE* 4.4 12.6 - - + +
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Residues in contact with PHE 94 (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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209A LEU* 4.1 14.8 - - + -
210A PRO* 3.9 22.9 - - + -
211A ASP* 6.4 0.2 - - + -
92B LYS* 3.6 41.7 - - + -
93B LEU* 1.3 75.5 - - - +
95B ARG* 1.3 60.8 + - - +
103B TRP* 3.6 31.2 - - + -
104B LYS 3.3 7.4 - - - +
105B GLU* 3.5 34.1 - - + -
106B ARG* 4.8 0.7 - - - -
174B PHE* 3.4 13.2 - - - -
175B ALA* 2.7 43.0 + - + +
177B ARG* 3.6 32.5 - - + -
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Residues in contact with ARG 95 (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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32A THR* 4.4 23.6 + - - +
34A GLU* 4.4 5.7 + - - +
94B PHE* 1.3 76.9 - - - +
96B PHE* 1.3 66.8 + - - +
97B ASP* 3.6 22.2 + - - +
103B TRP* 3.6 3.1 - - - -
104B LYS* 2.9 70.2 + - - +
105B GLU 4.9 3.2 + - - -
106B ARG* 4.3 20.7 - - + +
172B PHE* 4.2 33.9 - - + -
173B THR 3.6 4.9 - - - +
174B PHE* 4.2 9.6 - - + -
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Residues in contact with PHE 96 (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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200A ASP* 3.7 21.5 - - - -
203A VAL* 3.7 30.7 - - + -
204A ALA* 4.0 15.9 - - + -
207A THR* 3.8 24.5 - - + -
95B ARG* 1.3 76.0 + - - +
97B ASP* 1.3 58.2 + - - +
98B ALA* 3.6 24.0 + - + -
101B LYS* 3.8 15.7 - - - -
102B GLU 3.8 24.0 - - - -
103B TRP* 3.5 34.9 - + + -
172B PHE* 5.9 1.7 - - - -
173B THR* 3.1 26.6 + - - +
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Residues in contact with ASP 97 (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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95B ARG* 3.6 16.7 + - - +
96B PHE* 1.3 70.1 - - - +
98B ALA* 1.3 51.9 + - - +
99B ASP* 3.1 16.8 + - - +
100B ALA* 3.1 24.1 + - + +
101B LYS* 2.7 31.2 + - - -
102B GLU 3.0 21.6 + - - +
104B LYS* 3.5 37.3 + - + -
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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