Contacts of the strand formed by residues 102 - 120 (chain B) in PDB entry 3I5D
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 PHE 102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR* 3.8 38.8 - - + +
71B VAL* 3.6 28.3 - - + -
94B ILE* 4.8 10.8 - - + -
96B PRO 5.6 0.7 - - - -
98B GLU* 4.9 8.7 - - - +
100B GLY 4.3 0.4 - - - -
101B SER* 1.3 76.2 - - - +
103B PHE* 1.3 59.8 + - - +
104B VAL* 3.8 13.2 - - + -
190B VAL* 3.7 26.0 - - + -
192B ILE* 5.2 2.7 - - + -
235B LEU* 4.5 2.5 - - + -
238B ILE* 5.8 0.2 - - + -
258B VAL* 5.9 1.1 - - + -
321B ARG* 3.6 4.3 - - - +
322B PHE* 2.7 81.4 + + + -
324B VAL* 4.7 7.9 - - + -
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.4 28.8 - - - +
95B PRO* 3.3 36.1 - - + +
96B PRO* 5.0 2.5 + - + +
102B PHE* 1.3 76.4 - - - +
104B VAL* 1.3 62.8 + - - +
105B LEU* 4.1 15.7 - - + -
295B TYR* 3.6 32.8 - + + +
297B PHE* 3.5 27.1 - + + -
299B PHE* 5.6 0.2 - + - -
317B GLY 4.4 4.9 - - - -
318B TYR 4.1 6.1 - - - -
319B GLY* 3.6 37.0 - - - -
320B ILE 3.8 10.8 - - - -
321B ARG* 4.0 9.6 - - + +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.7 3.1 - - + -
89B VAL* 4.3 0.2 - - + -
93B ILE* 3.8 17.9 - - + -
94B ILE* 4.7 8.7 - - + -
102B PHE* 3.8 29.2 - - + -
103B PHE* 1.3 75.2 - - - +
105B LEU* 1.3 70.9 + - - +
106B THR* 3.4 4.9 + - + +
185B ALA* 4.4 7.2 - - + -
188B PHE* 4.2 13.9 - - + -
235B LEU* 3.9 21.5 - - + -
246B PHE* 5.5 0.4 - - + -
319B GLY* 3.3 2.6 - - - -
320B ILE* 3.2 32.2 + - + +
322B PHE* 3.9 14.1 - - + -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 4.3 11.0 - - + -
92B TYR* 4.4 10.5 - - + +
93B ILE* 3.0 29.6 + - - +
95B PRO* 4.6 2.9 - - + -
103B PHE* 3.8 15.2 + - + -
104B VAL* 1.3 78.0 - - - +
106B THR* 1.3 62.4 + - - +
107B ASN 3.4 12.1 - - - +
108B MET* 3.2 31.9 - - + -
182B LEU* 3.4 18.7 - - + +
185B ALA* 4.6 1.4 - - - +
299B PHE* 4.5 20.4 - - + -
315B ILE* 5.4 0.2 - - + -
317B GLY* 3.7 19.1 - - - -
318B TYR 3.1 21.3 - - - +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.7 11.4 - - + +
105B LEU* 1.3 78.9 - - - +
107B ASN* 1.3 58.9 + - - +
180B PRO* 3.3 10.9 - - - +
182B LEU* 2.9 35.4 + - - +
185B ALA* 3.7 22.9 - - + -
246B PHE* 4.0 8.5 - - + -
250B ALA* 3.1 39.6 + - + -
318B TYR 3.0 3.3 + - - -
319B GLY* 2.9 21.1 + - - -
320B ILE* 4.3 6.7 - - + -
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 3.4 6.8 - - - +
106B THR* 1.3 75.5 - - - +
108B MET* 1.3 70.7 + - - +
176B PRO* 3.7 8.4 - - - +
177B PRO* 2.7 29.7 + - - +
180B PRO* 3.3 9.4 - - - +
181B LEU* 3.1 32.1 + - - +
182B LEU 4.9 0.2 - - - +
250B ALA 3.4 11.9 - - - +
251B VAL* 2.9 32.2 + - - +
318B TYR* 2.8 34.8 + - + +
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Residues in contact with MET 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B TRP* 3.2 39.9 - - + -
105B LEU* 3.2 33.4 - - + -
107B ASN* 1.3 84.2 + - - +
109B ILE* 1.3 65.5 + - - +
110B ILE* 3.5 24.5 - - + -
177B PRO* 3.3 24.8 - - - +
181B LEU* 3.7 24.9 - - + +
182B LEU* 3.5 15.0 - - + -
315B ILE* 4.6 9.2 - - + -
316B LYS 3.3 11.0 - - - +
317B GLY* 4.5 4.0 - - - -
318B TYR* 4.1 2.1 - - - -
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Residues in contact with ILE 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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108B MET* 1.3 80.6 - - - +
110B ILE* 1.3 65.6 + - - +
111B THR* 3.7 6.7 + - - +
171B GLU* 4.7 20.9 - - + +
172B LYS* 5.1 3.1 - - + +
174B VAL* 3.5 44.2 - - + +
176B PRO* 4.0 19.1 - - + -
177B PRO* 4.3 1.8 - - + -
314B LEU 4.0 0.5 - - - +
316B LYS* 3.1 34.4 + - + +
318B TYR* 3.6 29.4 - - + +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 6.2 3.1 - - + -
82B LEU* 5.4 13.0 - - + -
87B TRP* 4.3 12.8 - - + -
108B MET* 3.5 35.9 - - + -
109B ILE* 1.3 75.1 - - - +
111B THR* 1.3 62.1 + - - +
112B THR* 3.7 26.2 + - + +
181B LEU* 5.7 2.5 - - + -
313B THR* 3.9 15.9 - - + -
314B LEU 3.7 4.0 - - - +
315B ILE* 4.6 16.8 - - + +
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 4.3 3.5 + - - +
110B ILE* 1.3 73.8 - - - +
112B THR* 1.3 64.5 + - - +
114B GLN* 3.6 29.6 - - + +
169B PRO* 3.9 5.6 - - + +
170B LEU 3.7 20.4 - - - +
171B GLU* 3.3 29.1 + - - +
172B LYS 4.7 1.6 + - - +
312B ARG 4.5 0.3 - - - +
313B THR* 3.5 2.8 - - - +
314B LEU* 2.7 47.9 + - - +
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 3.7 23.9 + - + +
111B THR* 1.3 79.6 - - - +
113B ASN* 1.3 76.7 + - - +
114B GLN* 3.0 6.8 + - - +
169B PRO* 4.0 10.7 - - - +
313B THR* 4.0 16.6 - - + +
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Residues in contact with ASN 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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112B THR* 1.3 80.9 - - - +
114B GLN* 1.3 63.6 + - - +
115B THR* 3.7 1.5 + - - +
168B CYS 3.4 8.1 - - - +
169B PRO* 3.5 8.5 - - + +
311B THR* 4.6 16.7 - - - +
312B ARG 3.9 5.3 + - - -
313B THR* 4.5 3.2 + - - -
402B NAG 1.5 83.6 + - + +
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Residues in contact with GLN 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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111B THR* 3.6 19.0 - - + +
112B THR 3.0 9.0 + - - +
113B ASN* 1.3 78.1 - - - +
115B THR* 1.3 59.8 + - - +
167B TRP* 3.4 21.2 + - + +
168B CYS 3.2 5.2 - - - +
169B PRO 3.1 27.7 + - - +
171B GLU 4.3 6.7 - - - +
311B THR* 3.1 8.1 - - - -
312B ARG* 2.7 81.9 + - + +
314B LEU* 3.3 25.4 - - - +
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Residues in contact with THR 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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113B ASN* 3.9 8.5 - - - +
114B GLN* 1.3 82.6 - - - +
116B GLN* 1.3 65.4 + - - +
117B SER* 3.1 8.7 + - - -
167B TRP* 3.7 11.0 - - - -
168B CYS* 2.8 34.4 + - - +
310B GLU 3.8 6.5 - - - +
311B THR* 3.4 26.2 - - + -
402B NAG 3.8 32.3 + - - +
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Residues in contact with GLN 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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115B THR* 1.3 72.2 + - - +
117B SER* 1.3 62.1 + - - +
165B LEU* 5.5 1.7 - - - +
166B SER* 3.5 13.9 + - - +
167B TRP* 3.4 37.1 - - + +
310B GLU* 4.7 5.1 + - + +
84C GLU 5.6 3.6 - - - +
85C ARG* 4.2 12.5 - - + +
86C ILE* 2.8 49.0 + - - +
92C TYR* 5.1 1.4 - - - -
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Residues in contact with SER 117 (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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115B THR* 3.1 15.2 + - - -
116B GLN* 1.3 77.7 + - - +
118B LYS* 1.3 77.6 + - - +
165B LEU* 3.1 5.4 - - - +
166B SER 2.8 34.9 + - - +
168B CYS* 3.6 15.4 - - - +
402B NAG 4.9 8.1 + - - -
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Residues in contact with LYS 118 (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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117B SER* 1.3 87.4 + - - +
119B CYS* 1.3 64.2 + - - +
149B THR* 3.9 23.6 - - + -
151B ARG* 5.4 12.5 - - - +
163B GLU* 3.0 34.3 - - + +
164B VAL 3.3 4.5 - - - -
165B LEU* 3.8 21.1 - - + +
168B CYS* 4.2 0.3 - - - +
84C GLU* 3.3 25.3 + - - -
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Residues in contact with CYS 119 (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* 1.3 76.5 - - - +
120B ALA* 1.3 63.8 + - - +
153B VAL* 4.6 1.6 - - - -
163B GLU* 3.3 9.5 - - - +
164B VAL* 2.7 43.1 + - - +
168B CYS* 2.0 44.0 - - + -
169B PRO* 5.6 1.8 - - + -
170B LEU* 3.3 26.7 - - - -
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Residues in contact with ALA 120 (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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119B CYS* 1.3 78.7 - - - +
121B GLU* 1.3 68.2 + - - +
122B ASN* 5.1 0.3 - - - +
153B VAL* 4.0 21.5 - - + +
154B SER 4.0 3.4 - - - +
155B TYR* 3.7 35.3 - - + -
161B THR* 3.9 6.3 - - + -
162B CYS 4.0 1.1 - - - -
164B VAL* 4.6 0.7 - - - -
170B LEU* 3.9 16.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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