Contacts of the strand formed by residues 110 - 118 (chain G) in PDB entry 1DE4
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 THR 110 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102G CYS* 3.7 21.3 - - + -
103G GLU 3.4 6.3 - - - +
104G MET* 3.9 18.8 - - + +
105G GLN* 6.3 0.2 - - - -
108G ASN 3.5 8.3 + - - -
109G SER* 1.3 79.0 + - - +
111G GLU* 1.3 78.8 + - - +
112G GLY 4.5 0.4 - - - +
161G LEU 4.4 4.3 - - - +
162G GLU* 5.7 1.6 - - - -
166G PRO* 3.9 21.1 - - + +
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Residues in contact with GLU 111 (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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102G CYS* 3.1 3.3 - - - -
103G GLU* 2.8 46.8 + - + +
105G GLN* 6.0 2.7 - - + +
110G THR* 1.3 81.7 - - - +
112G GLY* 1.3 70.7 + - - +
113G TYR* 4.4 4.7 - - + -
129G ASP* 5.7 0.7 - - - +
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Residues in contact with GLY 112 (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 3.4 7.9 - - - -
102G CYS* 4.2 2.7 - - - -
110G THR* 4.3 1.7 - - - +
111G GLU* 1.3 85.8 + - - +
113G TYR* 1.3 64.8 + - - +
128G PRO* 4.5 14.3 - - - +
161G LEU* 4.1 23.8 - - - -
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Residues in contact with TYR 113 (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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7G SER* 4.9 5.4 - - - -
8G LEU 3.9 3.1 + - - -
9G HIS* 3.0 27.9 + - + +
99G ILE* 4.0 30.0 - - + +
100G LEU* 3.1 11.7 - - - +
101G GLY* 2.9 60.4 + - - +
102G CYS* 3.8 11.5 + - - -
103G GLU* 4.5 11.2 - - + -
111G GLU* 4.4 6.5 - - + -
112G GLY* 1.3 77.7 - - - +
114G TRP* 1.3 64.1 + - - +
115G LYS* 5.0 14.8 - - + +
126G PHE 5.5 4.0 - - - -
128G PRO* 5.7 0.2 - - - -
161G LEU* 3.6 9.5 - - - +
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Residues in contact with TRP 114 (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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72G TRP* 4.0 15.9 - - - -
75G MET* 3.6 25.8 - - + -
76G PHE* 3.7 20.8 - + - -
98G VAL* 3.8 8.8 - - + +
99G ILE 3.3 5.2 - - - -
100G LEU* 3.9 14.6 - - + -
113G TYR* 1.3 76.4 - - - +
115G LYS* 1.3 65.1 + - - +
116G TYR* 3.2 36.9 + + - -
124G LEU 4.3 0.2 - - - +
125G GLU* 4.5 0.5 - - - +
126G PHE* 3.0 49.6 + - + +
133G TRP* 5.5 0.2 - - - -
157G ASN* 3.3 51.1 - - + -
160G TYR* 4.2 19.1 - + + -
161G LEU* 4.1 18.8 - - + -
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Residues in contact with LYS 115 (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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97G GLN 3.7 0.2 - - - +
98G VAL* 3.1 10.0 - - - +
99G ILE* 2.8 51.8 + - + +
113G TYR* 5.0 15.1 - - + +
114G TRP* 1.3 80.7 - - - +
116G TYR* 1.3 63.2 + - - +
122G ASP* 5.2 11.0 - - - +
124G LEU 3.6 4.9 - - - +
125G GLU* 3.0 42.6 + - + +
60H TRP* 3.7 20.7 - - + -
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Residues in contact with TYR 116 (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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75G MET* 4.6 2.9 - - - +
76G PHE* 3.4 11.2 - + - -
79G ASP* 2.9 31.9 + - + -
83G ILE* 4.5 4.7 - - + -
96G LEU* 4.3 19.3 - - + -
97G GLN 3.4 3.4 - - - -
98G VAL* 3.7 23.3 - - + -
114G TRP* 3.2 38.7 + + - -
115G LYS* 1.3 77.2 - - - +
117G GLY* 1.3 59.0 + - - +
118G TYR 4.1 0.4 - - - -
122G ASP* 4.2 0.2 - - - -
123G HIS* 3.1 26.9 + - + -
124G LEU* 2.9 32.6 + - + +
133G TRP* 4.6 6.1 - + - -
147G TRP* 3.5 37.0 - + - -
153G ARG* 5.1 1.2 + - - -
157G ASN* 5.0 2.2 + - - -
60H TRP* 4.0 7.3 - - - -
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Residues in contact with GLY 117 (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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95G THR 3.6 0.7 - - - +
96G LEU* 3.3 7.5 - - - +
97G GLN* 2.7 43.6 + - - +
116G TYR* 1.3 73.6 - - - +
118G TYR* 1.3 62.9 + - - -
119G ASP 3.7 0.5 + - - -
120G GLY 4.3 3.9 + - - -
121G GLN 3.3 11.0 - - - -
60H TRP* 4.0 21.0 - - - -
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Residues in contact with TYR 118 (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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80G PHE* 4.0 12.6 - + - -
83G ILE* 3.7 21.5 - - + -
84G MET* 3.3 14.8 - - + +
87G HIS* 3.3 41.1 - + - -
89G HIS* 2.6 24.6 + + - -
94G HIS* 3.1 27.0 - - + -
95G THR 3.4 11.0 - - - -
96G LEU* 4.2 9.6 - - + +
117G GLY* 1.3 70.7 - - - +
119G ASP* 1.3 89.5 + - + +
120G GLY 3.1 1.3 - - - -
121G GLN* 3.0 23.1 + - - +
123G HIS* 3.8 28.1 - + + +
137G GLU* 5.6 2.0 - - - +
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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