Contacts of the strand formed by residues 107 - 111 (chain G) in PDB entry 3HOU
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 LYS 107 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G TYR* 5.1 0.2 + - - -
92G VAL* 4.4 17.5 - - + +
100G GLU* 3.6 34.6 + - + +
101G VAL 3.5 4.9 - - - +
102G GLN* 3.1 34.8 - - + +
105G PRO 5.6 0.9 - - - +
106G MET* 1.3 87.9 - - - +
108G VAL* 1.3 62.9 + - - +
157G ILE 4.5 1.6 + - - -
158G HIS* 3.0 32.3 - - + -
159G ALA 3.6 2.1 + - - -
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Residues in contact with VAL 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G VAL* 4.9 1.1 - - + -
100G GLU* 3.2 6.9 - - - +
101G VAL* 2.8 41.6 + - + +
102G GLN* 4.8 0.2 - - - +
103G VAL* 4.4 16.4 - - + -
106G MET* 4.0 22.9 - - + -
107G LYS* 1.3 77.5 - - - +
109G PHE* 1.3 65.6 + - - +
110G VAL* 5.1 1.1 - - + -
145G VAL* 4.0 21.1 - - + -
147G ILE* 4.4 13.5 - - + -
158G HIS* 4.4 0.2 - - - -
159G ALA* 3.5 17.7 - - + +
160G ILE 4.1 2.5 - - - -
161G GLY* 3.8 21.3 - - - +
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Residues in contact with PHE 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G HIS* 3.9 8.5 - - + -
98G GLY* 3.4 39.7 - - - -
99G PHE 3.1 15.7 - - - -
100G GLU* 4.0 4.9 - - + +
108G VAL* 1.3 75.1 - - - +
110G VAL* 1.3 64.4 + - - +
111G THR* 4.1 12.3 - - - -
158G HIS* 4.2 11.7 - - - +
159G ALA 2.8 15.8 + - - +
160G ILE* 3.0 18.9 - - + +
161G GLY 2.8 23.5 + - - -
97S HIS* 3.4 52.0 - + + -
109S PHE* 3.9 18.4 - + - -
111S THR* 4.0 14.4 - - - -
113S HIS* 4.7 5.4 - + + +
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Residues in contact with VAL 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLY* 3.1 24.1 - - - -
99G PHE* 3.0 44.2 + - + +
101G VAL* 4.8 2.5 - - + -
108G VAL* 5.1 1.3 - - + -
109G PHE* 1.3 77.5 - - - +
111G THR* 1.3 62.2 + - - +
114G LEU 4.4 4.3 - - - +
115G MET* 3.7 28.6 - - + +
145G VAL* 4.1 22.2 - - + -
161G GLY 3.3 25.1 - - - +
163G ILE* 4.2 11.4 - - + -
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Residues in contact with THR 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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97G HIS 3.4 6.8 + - - -
109G PHE* 3.9 16.8 + - - -
110G VAL* 1.3 74.5 - - - +
112G LYS* 1.3 56.8 + - - +
113G HIS* 3.0 30.9 + - + -
114G LEU* 2.6 79.0 + - + +
115G MET* 4.1 0.7 - - - -
160G ILE* 4.3 3.8 - - + -
109S PHE* 4.4 5.5 - - - -
160S ILE* 4.1 22.4 - - + -
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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