Contacts of the strand formed by residues 122 - 129 (chain G) in PDB entry 5UQ9
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 LEU 122 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G GLY* 3.2 31.2 - - - +
96G ASP 3.0 9.0 + - - +
97G ILE* 3.2 43.1 - - + +
98G ILE 3.2 4.5 + - - +
116G LEU* 4.1 1.1 - - - -
117G LYS* 4.1 11.7 - - + +
120G GLY 4.6 4.9 - - - +
121G ILE* 1.3 78.9 - - - +
123G PHE* 1.3 62.1 + - - +
124G VAL* 4.0 2.1 + - - +
146G ASN* 3.5 26.5 - - + +
148G GLU* 3.5 35.2 - - + +
149G ALA* 4.8 2.0 - - + +
152G HIS* 5.6 2.5 - - + -
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Residues in contact with PHE 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G VAL* 5.1 0.4 - - + -
85G ILE* 3.7 19.1 - - + -
98G ILE* 3.4 31.4 - - + +
100G ASP* 3.5 29.2 - - + -
109G THR* 3.5 32.1 - - + -
112G ARG* 3.9 25.1 - - + -
113G CYS* 4.0 26.7 - - + -
116G LEU* 3.5 36.3 - - + +
122G LEU* 1.3 72.8 - - - +
124G VAL* 1.3 67.3 + - - +
125G GLY 4.3 4.3 - - - -
145G GLY* 3.6 5.0 - - - -
146G ASN* 3.4 23.3 + - - +
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Residues in contact with VAL 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ILE 3.1 9.9 + - - +
99G ILE* 3.3 22.8 - - + +
100G ASP* 2.8 26.5 + - - +
122G LEU 4.9 0.4 - - - +
123G PHE* 1.3 85.3 - - - +
125G GLY* 1.3 63.6 + - - +
126G SER 4.3 0.4 - - - +
143G PRO* 4.3 13.5 - - + -
144G GLY 3.5 20.9 - - - +
146G ASN* 3.6 13.5 - - + +
149G ALA* 3.5 31.9 - - + -
153G ILE* 4.3 7.2 - - + -
173G TRP* 3.9 9.4 - - + -
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Residues in contact with GLY 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G ASP* 3.6 2.2 - - - -
109G THR* 3.7 17.4 - - - +
123G PHE* 4.3 2.9 - - - -
124G VAL* 1.3 69.9 - - - +
126G SER* 1.3 60.7 + - - -
142G MET 3.5 3.3 - - - +
144G GLY* 2.7 31.3 + - - +
145G GLY* 4.7 0.2 - - - -
180G GLY* 4.2 9.0 + - - -
181G HIS* 3.5 27.5 + - - -
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Residues in contact with SER 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G ILE* 4.3 17.0 - - - -
100G ASP 2.9 20.0 + - - +
101G GLY* 3.3 16.5 - - - -
102G GLY 4.0 0.2 - - - +
124G VAL* 3.7 1.7 + - - -
125G GLY* 1.3 74.1 - - - +
127G GLY* 1.3 64.8 + - - +
128G VAL* 4.7 4.3 - - - +
141G LEU* 4.0 8.1 - - - +
142G MET 3.2 11.5 + - - -
143G PRO* 3.4 27.7 - - - +
157G PHE* 4.2 7.6 - - - -
181G HIS* 3.1 9.7 + - - -
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Residues in contact with GLY 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G GLY 5.0 0.9 - - - -
102G GLY 5.2 1.1 - - - -
103G ASN* 6.0 0.4 - - - -
126G SER* 1.3 73.5 + - - +
128G VAL* 1.3 60.3 + - - +
140G SER 3.6 0.9 - - - +
141G LEU* 3.2 7.8 - - - -
142G MET* 2.8 49.5 + - - +
180G GLY 5.1 0.2 + - - -
181G HIS* 4.0 11.9 - - - -
184G LYS* 4.2 18.8 - - - -
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Residues in contact with VAL 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G MET* 4.5 23.8 - - + -
18G LEU* 5.4 11.9 - - + -
74G LEU* 5.2 4.7 - - + -
76G LYS* 5.4 0.9 - - - +
101G GLY* 3.2 28.5 + - - +
103G ASN* 4.6 6.7 + - - +
126G SER* 4.7 7.0 - - - +
127G GLY* 1.3 78.1 - - - +
129G SER* 1.3 60.0 + - - +
139G PRO* 5.5 4.3 - - + -
140G SER 3.6 3.4 - - - -
141G LEU* 3.6 24.2 - - + -
184G LYS* 3.3 22.2 + - - +
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Residues in contact with SER 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G VAL* 1.3 77.0 - - - +
130G GLY* 1.3 61.4 + - - +
131G GLY 3.8 1.1 - - - -
135G ALA* 5.6 0.4 - - - -
139G PRO* 3.5 21.5 - - - +
140G SER 3.4 13.4 + - - -
142G MET* 4.9 1.8 - - - -
184G LYS* 4.4 4.4 - - - +
187G HIS* 3.4 26.2 + - - -
191G GLU* 5.1 0.3 + - - -
365G GLY 4.0 5.1 - - - +
366G CYS* 3.7 31.2 - - - -
367G ILE* 4.2 9.4 + - - +
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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