Contacts of the strand formed by residues 109 - 113 (chain G) in PDB entry 2NOQ
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 ALA 109 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G MET* 3.2 26.0 - - + -
64G SER 3.2 4.8 + - - +
65G ILE* 3.4 12.9 - - + -
66G CYS 3.1 20.7 + - - -
107G TYR* 4.0 3.6 - - - +
108G ASN* 1.4 77.4 - - - +
110G PHE* 1.4 72.1 + - - +
111G ILE* 5.7 1.1 - - + -
136G THR* 6.3 1.8 - - + -
151G VAL* 5.0 6.5 - - + -
154G THR* 4.5 2.9 - - - +
156G LYS* 4.1 12.3 - - - +
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Residues in contact with PHE 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G CYS* 3.5 36.6 - - + +
68G PHE* 6.3 1.8 - - + -
85G MET* 5.4 8.1 - - + -
100G ILE* 6.4 0.2 - - + -
103G LEU* 4.0 22.0 - - + -
104G SER* 3.9 24.7 - - - -
107G TYR* 4.1 10.8 - - + -
109G ALA* 1.4 80.6 - - - +
111G ILE* 1.3 64.2 + - - +
124G LEU* 6.5 0.2 - - + -
128G LEU* 4.4 15.7 - - + -
133G LYS* 3.2 44.5 + - + -
134G PHE 4.6 1.3 + - - +
135G PRO* 3.4 26.7 - - + +
136G THR* 3.0 26.9 + - - +
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Residues in contact with ILE 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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65G ILE* 3.9 22.7 - - + -
66G CYS 2.9 9.0 + - - +
67G ILE* 3.4 11.9 - - + +
68G PHE* 2.9 24.3 + - - +
73G ASP* 5.3 0.2 - - - +
109G ALA* 5.7 1.8 - - + -
110G PHE* 1.3 78.9 - - - +
112G ALA* 1.3 66.1 + - - +
135G PRO* 4.2 0.6 - - - +
136G THR* 3.4 20.2 - - - +
138G VAL* 3.6 31.9 - - + -
144G LEU* 5.2 12.3 - - + -
147G LYS* 4.7 15.7 - - + -
148G VAL* 4.6 18.4 - - + +
151G VAL* 5.1 12.6 - - + -
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Residues in contact with ALA 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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68G PHE* 3.3 25.6 - - + +
73G ASP* 4.6 0.9 - - - -
111G ILE* 1.3 76.9 - - - +
113G SER* 1.4 72.5 + - - +
117G ILE* 5.2 5.6 - - + -
120G VAL* 4.9 8.5 - - + -
135G PRO* 3.7 21.1 - - + +
136G THR 2.8 10.1 + - - +
137G PRO* 3.3 3.5 - - - +
138G VAL* 3.1 26.7 + - - +
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Residues in contact with SER 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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68G PHE 2.9 9.9 + - - -
69G GLY* 3.3 15.2 - - - -
70G ASP 4.0 3.6 + - - -
73G ASP* 3.1 24.2 + - - +
112G ALA* 1.4 74.2 - - - +
114G GLU* 1.3 66.2 + - - +
115G VAL* 4.5 4.3 - - - -
116G LEU* 3.1 37.2 + - - +
117G ILE* 3.7 3.1 + - - +
138G VAL* 3.7 6.7 - - - -
140G HIS* 4.3 20.3 + - - +
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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