Contacts of the strand formed by residues 102 - 116 (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 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU* 5.0 0.5 - - - +
36A GLU* 4.7 9.2 - - - +
38A LYS* 4.0 25.7 + - - -
207A THR* 4.6 4.5 - - - -
96B PHE* 3.8 8.2 - - - -
97B ASP* 3.0 28.0 + - + +
100B ALA* 3.8 29.2 - - + +
101B LYS* 1.3 78.9 - - - +
103B TRP* 1.3 69.5 + - - +
104B LYS* 4.0 22.1 - - - +
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Residues in contact with TRP 103 (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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204A ALA* 3.1 40.4 + - + -
207A THR* 2.8 38.9 + - + +
208A ALA 3.6 15.0 - - - -
209A LEU* 3.6 16.1 - - + +
210A PRO* 3.8 26.9 - - + +
94B PHE* 3.6 22.2 - - + -
95B ARG 3.8 2.9 - - - -
96B PHE* 3.5 24.7 - + + -
102B GLU* 1.3 83.1 - - - +
104B LYS* 1.3 64.0 + - - +
149B ASN* 4.3 0.4 - - - -
157B VAL* 4.0 15.7 - - + -
173B THR* 3.4 24.9 - - + -
174B PHE 4.0 0.4 - - - -
175B ALA* 3.4 28.7 - - + -
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Residues in contact with LYS 104 (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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34A GLU* 3.4 34.8 + - + +
36A GLU* 5.1 2.2 + - - -
94B PHE* 3.3 4.2 - - - -
95B ARG* 2.9 73.1 + - - +
97B ASP* 3.5 29.8 + - + +
100B ALA* 5.3 3.8 - - - +
102B GLU* 4.0 25.4 - - - +
103B TRP* 1.3 79.5 - - - +
105B GLU* 1.3 65.8 + - - +
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Residues in contact with GLU 105 (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* 2.8 30.0 + - - +
32A THR 3.7 2.4 - - - +
33A GLY 3.5 12.1 - - - +
34A GLU* 3.2 26.5 + - - +
35A PHE* 4.0 17.1 - - - +
210A PRO* 5.5 4.0 - - + +
211A ASP* 4.5 13.2 - - - +
92B LYS* 3.2 34.1 + - + +
93B LEU 3.6 6.3 - - - +
94B PHE* 3.5 26.5 - - + -
95B ARG* 4.9 2.8 + - - -
104B LYS* 1.3 76.5 - - - +
106B ARG* 1.3 59.8 + - - +
107B GLY 4.7 2.9 - - - +
108B THR* 4.8 1.4 + - - -
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Residues in contact with ARG 106 (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 3.7 12.6 - - - +
33A GLY* 4.2 3.6 - - - -
93B LEU* 2.7 26.1 + - + +
95B ARG* 4.3 20.8 - - + +
104B LYS 3.5 0.2 + - - -
105B GLU* 1.3 73.5 - - - +
107B GLY* 1.3 55.7 + - - +
128B ARG* 2.9 32.1 + - - +
135B CYS* 3.1 32.6 + - + +
163B ASP* 2.8 26.3 + - - -
165B ALA* 4.3 3.6 - - - -
166B GLU* 3.6 36.1 + - - +
172B PHE* 3.3 34.3 - - - -
174B PHE* 3.2 29.4 - - - -
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Residues in contact with GLY 107 (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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33A GLY* 4.6 4.7 + - - -
92B LYS* 3.7 0.7 - - - +
93B LEU* 2.9 27.3 + - - +
105B GLU* 3.8 2.8 - - - +
106B ARG* 1.3 81.3 - - - +
108B THR* 1.3 64.6 + - - -
126B MET* 3.4 9.2 - - - +
128B ARG* 3.8 17.7 - - - -
135B CYS* 3.9 6.5 - - - -
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Residues in contact with THR 108 (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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154A ASN* 5.4 10.2 + - - -
216A LEU* 3.7 23.8 - - + -
90B ARG* 3.9 11.4 - - - +
91B ALA 3.5 12.6 - - - +
92B LYS* 2.9 35.8 + - - +
105B GLU* 4.8 2.3 + - - +
107B GLY* 1.3 74.9 - - - -
109B GLY* 1.3 62.3 + - - +
126B MET* 4.2 0.2 - - - -
127B ARG 4.1 2.5 - - - -
128B ARG* 3.5 5.8 - - - +
129B ASP* 3.1 29.0 + - - +
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Residues in contact with GLY 109 (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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90B ARG* 3.4 11.1 - - - -
91B ALA 3.0 32.0 + - - +
108B THR* 1.3 77.4 - - - +
110B ASP* 1.3 66.7 + - - -
111B CYS 3.4 0.9 + - - -
126B MET* 3.7 6.4 - - - +
127B ARG 3.3 11.2 - - - -
129B ASP* 3.5 14.4 - - - -
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Residues in contact with ASP 110 (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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88B LYS* 4.4 27.2 + - + +
89B VAL 3.7 4.1 - - - -
90B ARG* 3.0 28.1 + - - +
109B GLY* 1.3 69.4 - - - -
111B CYS* 1.3 60.3 + - - +
112B LYS* 3.9 23.3 + - - +
125B LEU 3.8 2.1 - - - +
126B MET* 3.4 20.4 - - - -
127B ARG* 3.4 11.2 + - + +
129B ASP* 4.4 5.2 + - - +
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Residues in contact with CYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TYR* 4.0 1.0 - - - +
88B LYS* 3.4 2.9 - - - -
89B VAL* 2.7 44.4 + - + +
91B ALA* 4.6 2.7 - - + -
109B GLY 3.4 1.2 + - - -
110B ASP* 1.3 71.5 - - - +
112B LYS* 1.3 62.3 + - - +
113B PHE* 4.1 8.7 - - - -
124B ILE* 4.0 26.0 - - - -
125B LEU 3.8 3.1 - - - -
126B MET* 3.9 20.0 - - - -
176B ILE* 4.1 23.8 - - + -
187B PHE* 4.1 16.4 - - - -
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Residues in contact with LYS 112 (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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80B GLU* 5.1 11.9 + - - +
85B VAL* 4.7 12.5 - - + +
87B TYR 3.3 6.7 - - - +
88B LYS* 3.9 31.4 - - + +
110B ASP* 4.2 19.5 + - - +
111B CYS* 1.3 76.7 - - - +
113B PHE* 1.3 66.1 + - - +
114B LEU* 3.8 27.0 + - + -
123B ARG 3.5 0.7 - - - +
124B ILE* 3.4 6.6 - - - +
125B LEU* 2.9 41.9 + - + +
127B ARG* 6.4 1.6 - - - +
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Residues in contact with PHE 113 (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 3.6 0.5 - - - +
85B VAL* 3.7 3.1 - - - -
86B LEU* 2.9 35.4 + - + +
87B TYR* 2.9 37.9 + + + +
111B CYS* 4.1 6.1 - - - -
112B LYS* 1.3 78.6 - - - +
114B LEU* 1.3 61.2 + - - +
122B VAL* 3.9 11.9 - - + -
123B ARG 3.3 3.8 - - - -
124B ILE* 3.5 23.8 - - + -
140B ILE* 3.9 11.2 - - + -
187B PHE* 3.5 39.5 - + - -
190B GLU* 3.6 16.8 - - + -
191B PHE* 3.4 39.7 - + - -
194B ALA* 4.4 4.3 - - + -
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Residues in contact with LEU 114 (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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80B GLU* 4.1 12.1 - - + +
83B GLU* 3.3 36.3 - - + +
84B GLU 3.2 6.3 - - - +
85B VAL* 3.8 29.2 - - + -
112B LYS* 3.9 22.0 - - + -
113B PHE* 1.3 76.8 - - - +
115B LYS* 1.3 60.7 + - - +
116B ASN 3.8 1.1 + - - -
121B LYS 3.7 1.4 - - - +
122B VAL* 3.3 4.5 - - - +
123B ARG* 3.0 40.7 + - + +
125B LEU* 3.6 39.7 - - + -
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Residues in contact with LYS 115 (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* 3.4 3.4 - - - -
84B GLU* 2.9 67.8 + - + +
86B LEU* 3.9 27.1 - - + +
113B PHE 4.0 1.2 + - - -
114B LEU* 1.3 70.3 - - - +
116B ASN* 1.3 68.7 + - - +
117B LYS* 3.4 3.6 + - - +
120B ASN* 3.5 39.1 + - + +
121B LYS 3.6 3.4 - - - -
122B VAL* 3.9 14.1 - - + +
197B ILE* 4.6 10.7 - - + +
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Residues in contact with ASN 116 (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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82B ASP* 3.9 16.3 + - - +
83B GLU* 3.9 16.5 + - + +
114B LEU 3.8 2.4 + - - -
115B LYS* 1.3 73.6 - - - +
117B LYS* 1.3 55.9 + - - +
118B LYS* 2.6 40.0 + - - +
119B THR* 3.2 28.7 + - - +
120B ASN* 2.6 34.7 + - - +
121B LYS* 3.0 16.9 + - + +
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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