Contacts of the strand formed by residues 109 - 115 (chain B) in PDB entry 1ULH
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B VAL* 3.7 28.3 - - + +
102B ALA* 5.8 1.1 - - + -
103B TYR* 4.0 15.5 - + + -
107B LYS 5.0 0.4 - - - +
108B PRO* 1.3 79.2 - - + +
110B TYR* 1.3 71.3 + - - +
111B LEU* 4.0 7.4 - - + -
140B PHE* 3.6 47.6 - + + -
142B VAL* 3.3 46.7 - - + +
143B PRO* 3.7 6.0 - - - +
256B ILE* 3.8 6.5 - - - -
257B GLN* 3.2 30.5 - - + +
259B LEU* 3.5 34.5 - - + -
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Residues in contact with TYR 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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109B PHE* 1.3 84.8 - - - +
111B LEU* 1.3 71.1 + - - +
112B TYR* 4.3 0.4 - - + -
142B VAL* 4.5 0.7 - - - -
143B PRO* 3.4 28.9 - - + +
144B LEU* 5.5 0.2 - - - -
145B VAL* 3.9 19.3 - - + -
240B PRO 2.7 28.6 + - - -
241B SER 3.1 1.4 - - - -
242B PHE 2.9 26.6 + - - -
243B SER* 3.9 14.4 - - - -
246B PHE* 4.3 5.2 - + - -
250B PHE* 3.5 22.2 - + + -
256B ILE* 3.4 25.6 - - + -
257B GLN 3.0 28.3 + - - -
258B CYS* 3.7 17.3 - - + -
259B LEU 3.0 25.8 + - - -
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Residues in contact with LEU 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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109B PHE* 4.0 3.4 - - + -
110B TYR* 1.3 76.9 - - - +
112B TYR* 1.3 54.9 + - - +
133B THR* 3.6 15.0 - - + +
136B LEU* 3.5 28.9 - - + -
137B GLN* 3.5 23.1 - - + +
142B VAL* 3.8 16.2 - - + -
143B PRO 2.9 10.3 + - - +
144B LEU* 3.1 18.7 - - + -
145B VAL* 2.7 34.0 + - - +
259B LEU* 3.3 38.8 - - + +
261B PRO* 3.9 15.7 - - + -
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Residues in contact with TYR 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 TYR* 4.3 0.7 - - + -
111B LEU* 1.3 76.5 - - - +
113B THR* 1.3 94.8 + - - +
114B GLY* 4.7 1.1 - - - -
144B LEU* 4.4 0.4 - - - -
145B VAL* 3.3 20.9 - - + -
147B GLN* 3.0 25.8 + - + -
188B PHE* 5.6 0.2 - + - -
237B GLN* 2.6 33.2 + - - +
240B PRO* 3.3 41.0 - - + +
241B SER* 3.6 17.0 - - - -
258B CYS* 3.9 14.8 - - - -
259B LEU 3.0 6.7 + - - -
260B ILE* 3.1 49.3 - - + +
261B PRO* 3.3 3.5 - - - +
270B PHE* 3.6 17.2 - + - -
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Residues in contact with THR 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 TYR* 1.3 86.2 - - - +
114B GLY* 1.3 64.2 + - - +
129B PRO* 5.0 7.1 - - + +
130B PHE* 4.0 26.8 - - + -
133B THR* 4.3 21.0 + - + +
144B LEU* 4.2 1.5 - - + +
145B VAL 3.0 6.3 + - - +
146B ILE* 3.1 19.9 - - + -
147B GLN 3.0 21.0 + - - -
260B ILE* 4.6 3.8 - - - -
261B PRO* 2.7 31.3 + - - -
262B CYS* 4.8 1.9 - - - +
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Residues in contact with GLY 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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112B TYR* 4.7 1.8 - - - -
113B THR* 1.3 84.0 + - - +
115B ARG* 1.3 64.0 + - - +
130B PHE* 3.8 12.9 - - - -
146B ILE* 4.5 2.5 - - - -
147B GLN* 3.3 14.4 - - - -
149B THR* 6.3 0.4 - - - -
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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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114B GLY* 1.3 77.2 - - - +
116B GLY* 1.3 80.9 + - - +
117B PRO* 3.1 16.3 - - - +
118B SER* 4.1 6.3 - - - +
119B SER* 4.0 13.5 + - - +
121B ALA 4.5 6.7 + - - -
122B MET* 3.6 23.5 - - - +
126B HIS* 3.3 32.8 + - - -
130B PHE* 3.8 20.2 - - + -
147B GLN 2.8 9.5 + - - -
148B MET* 3.4 13.8 - - + -
149B THR* 3.2 15.7 + - - +
171B ASN* 2.6 31.8 + - + +
175B ILE* 4.1 19.5 - - + -
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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
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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