Contacts of the strand formed by residues 107 - 116 (chain B) in PDB entry 1U1C
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 VAL 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B GLY 3.9 1.7 + - - +
106B ASP* 1.3 74.5 - - - +
108B LEU* 1.3 66.0 + - - +
109B VAL* 5.1 0.4 - - + -
144B ALA* 4.6 0.4 - - + -
149B ALA* 3.8 9.6 - - + -
150B THR 3.0 14.6 + - - +
151B THR* 3.3 24.8 - - + +
152B HIS* 3.1 24.1 + - - -
216B VAL* 3.5 27.6 - - + -
217B ALA 3.5 7.9 - - - +
240B HIS* 5.7 2.0 - - + -
241B ALA* 4.5 14.4 - - + +
244B ILE* 3.7 31.9 - - + -
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Residues in contact with LEU 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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95B THR* 3.8 5.4 - - + -
97B ALA* 4.9 0.7 - - + -
102B ILE* 3.8 18.4 - - + -
106B ASP* 4.8 0.2 - - + -
107B VAL* 1.3 74.1 - - - +
109B VAL* 1.3 62.1 + - - +
110B THR* 4.1 3.7 + - - +
152B HIS* 3.3 42.2 - - + -
193B MET* 3.9 19.1 - - + +
194B ASN* 3.5 41.5 - - + +
215B MET 4.0 0.2 - - - +
216B VAL* 3.3 5.8 - - - +
217B ALA* 2.9 40.0 + - + +
219B VAL* 3.7 23.6 - - + -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 5.1 1.3 - - + -
108B LEU* 1.3 74.6 - - - +
110B THR* 1.3 63.7 + - - +
137B THR* 3.9 27.8 - - + -
140B LEU* 4.0 33.9 - - + +
141B VAL* 4.1 8.3 - - + -
144B ALA* 5.3 0.2 - - + -
151B THR* 4.0 20.6 - - + -
152B HIS 2.9 6.9 + - - -
153B VAL* 3.3 14.5 - - + +
154B GLY 3.1 24.9 + - - +
193B MET* 3.7 2.9 - - - +
215B MET 3.6 9.4 - - - +
216B VAL* 3.9 16.2 - - + -
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Residues in contact with THR 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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108B LEU* 4.1 3.7 + - - +
109B VAL* 1.3 73.5 - - - +
111B THR* 1.3 60.4 + - - +
112B ALA* 3.3 28.0 - - - +
113B SER* 3.6 17.3 - - - +
132B ALA* 3.4 17.3 - - - +
137B THR* 4.0 4.7 + - - -
154B GLY 3.4 4.5 - - - +
156B THR* 2.6 28.3 + - - +
193B MET* 4.7 1.4 - - - +
194B ASN* 5.0 0.7 + - - -
203B LEU* 4.2 6.5 - - + -
215B MET* 3.0 40.9 + - + +
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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
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110B THR* 1.3 73.2 - - - +
112B ALA* 1.3 59.9 + - - +
131B VAL* 3.5 7.3 - - - +
132B ALA* 2.8 32.5 + - - +
137B THR* 4.5 10.8 - - + -
153B VAL* 3.6 29.8 - - + -
154B GLY* 3.0 22.6 + - - +
155B VAL* 4.1 1.0 + - - +
131F VAL* 4.0 24.2 - - - +
132F ALA 5.0 2.6 + - - +
134F PHE* 4.2 20.0 - - + +
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Residues in contact with ALA 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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110B THR* 3.3 6.7 - - - +
111B THR* 1.3 82.8 + - - +
113B SER* 1.3 63.8 + - - +
130B ALA 3.1 14.8 - - - +
131B VAL* 3.8 7.6 - - + -
155B VAL* 3.4 8.8 - - - +
156B THR 3.2 19.9 + - - -
203B LEU* 4.4 0.7 - - - -
129F PRO* 3.6 23.6 - - + -
131F VAL* 3.7 22.7 - - + -
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Residues in contact with SER 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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110B THR* 3.6 9.9 - - - +
112B ALA* 1.3 76.8 - - - +
114B VAL* 1.3 65.3 + - - +
115B ARG* 3.5 3.3 + - - +
130B ALA* 2.9 23.5 + - - +
156B THR* 3.1 9.5 + - - -
158B SER* 4.3 0.7 - - - -
199B SER* 2.7 32.8 + - - -
200B ALA* 4.0 20.6 - - - -
203B LEU* 3.7 2.6 - - - +
127F GLU 3.7 1.9 - - - +
129F PRO* 3.4 17.2 - - - +
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Residues in contact with VAL 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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113B SER* 1.3 71.1 - - - +
115B ARG* 1.3 61.6 + - - +
116B LEU* 3.1 13.6 + - + -
155B VAL* 3.7 19.3 - - + +
156B THR 2.7 17.7 + - - +
157B ALA* 3.9 11.9 - - + -
158B SER* 3.1 28.4 + - - +
187B TRP* 3.8 32.5 - - + -
192B VAL* 4.0 12.1 - - + -
200B ALA* 4.1 0.2 - - - +
127F GLU* 3.4 24.0 - - + +
128F PHE* 3.8 18.2 - - + +
129F PRO* 4.0 1.3 - - + -
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Residues in contact with ARG 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 SER 4.0 2.2 - - - +
114B VAL* 1.3 70.1 - - - +
116B LEU* 1.3 59.8 + - - +
117B ASP* 3.2 21.1 + - - +
120B SER* 2.9 41.0 + - - +
121B LEU* 3.3 12.7 - - - +
124B ALA 2.7 24.0 + - - -
125B PRO 2.8 19.1 + - - -
126B LEU* 3.3 28.6 + - + +
128B PHE* 2.7 40.2 + - - +
129B PRO* 5.3 0.2 - - - -
130B ALA* 3.8 23.1 - - + +
200B ALA* 4.1 5.2 - - + -
204B THR* 3.9 15.4 - - - +
127F GLU* 2.9 31.0 + - - +
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Residues in contact with LEU 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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122A HIS* 3.2 15.9 + - + -
114B VAL* 3.1 16.5 + - + +
115B ARG* 1.3 70.7 - - - +
117B ASP* 1.3 56.2 + - - +
157B ALA* 4.2 17.0 - - + -
158B SER 3.0 20.2 + - - +
159B SER* 3.9 8.5 - - - -
160B ASP 3.0 18.7 + - - -
165B GLY 4.2 10.3 - - - +
179B HIS* 6.0 1.1 - - - +
180B PHE* 4.1 29.6 - - + -
187B TRP* 3.6 44.4 - - + +
195B TYR* 4.5 2.7 - - + -
127F GLU* 4.0 16.2 - - + +
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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