Contacts of the strand formed by residues 71 - 77 (chain G) in PDB entry 3GUT
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 71 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70G GLY* 1.3 81.8 - - - +
72G VAL* 1.3 59.4 + - - +
101G GLU* 5.2 10.1 + - - +
102G ALA 3.5 10.8 - - - +
103G ASP* 3.3 20.9 - - - +
104G LEU* 3.8 8.5 - - - +
162G GLN 4.1 0.3 - - - +
163G VAL* 3.6 0.7 - - - -
164G THR* 2.6 54.5 + - - +
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Residues in contact with VAL 72 (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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61G ILE* 4.4 5.2 - - + -
71G THR* 1.3 73.1 - - - +
73G ARG* 1.3 62.2 + - - +
74G ILE* 3.8 22.0 - - + -
100G TYR* 3.9 8.0 - - + +
101G GLU* 3.1 8.7 - - - +
102G ALA* 3.1 29.8 + - + +
103G ASP 5.3 0.7 - - - +
104G LEU* 3.3 28.3 - - + -
113G PHE* 3.8 28.7 - - + -
161G PHE* 5.0 0.2 - - + -
162G GLN 3.5 10.3 - - - +
163G VAL* 4.2 16.6 - - + +
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Residues in contact with ARG 73 (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 VAL* 1.3 75.1 - - - +
74G ILE* 1.3 68.2 + - - +
99G TYR* 3.4 36.0 + - + -
100G TYR 3.1 10.5 - - - +
101G GLU* 3.1 32.7 + - + -
136G THR 4.9 3.0 + - - -
137G ASN 3.4 24.0 + - - -
138G ASN* 4.0 16.4 + - - +
160G CYS 3.3 3.8 - - - +
162G GLN* 2.9 65.5 + - + +
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Residues in contact with ILE 74 (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 VAL* 3.8 14.6 - - + -
73G ARG* 1.3 80.2 - - - +
75G SER* 1.3 62.6 + - - +
90G LEU* 3.3 21.4 - - + +
99G TYR* 3.4 2.4 - - - -
100G TYR* 2.6 65.4 + - + -
113G PHE* 4.6 10.3 - - + -
116G LEU* 4.7 7.9 - - + -
159G LEU* 4.1 21.1 - - + -
160G CYS 3.6 2.5 - - - +
161G PHE* 2.7 52.9 - - + -
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Residues in contact with SER 75 (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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73G ARG* 4.8 0.4 - - - -
74G ILE* 1.3 75.4 - - - +
76G LEU* 1.3 77.2 + - - +
77G VAL* 4.1 5.2 - - - +
90G LEU* 4.6 0.4 - - - -
99G TYR* 4.5 6.5 - - - -
138G ASN* 3.3 29.0 + - - -
140G PRO* 4.5 3.6 - - - +
158G ARG 3.4 2.3 - - - +
159G LEU* 3.5 1.4 - - - -
160G CYS* 2.6 44.1 + - - +
162G GLN* 3.1 24.6 - - - +
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Residues in contact with LEU 76 (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 SER* 1.3 83.1 + - - +
77G VAL* 1.3 61.3 + - - +
85G PRO* 3.7 4.0 - - - +
86G HIS* 3.1 18.7 + - + +
88G HIS* 3.4 47.6 - - + +
89G GLU 4.2 0.9 - - - -
90G LEU* 3.3 42.3 - - + +
98G GLY 4.8 7.5 + - - +
118G ILE* 4.2 9.9 - - + -
138G ASN* 4.5 2.8 + - - +
157G VAL* 4.0 23.3 - - + -
158G ARG 3.5 6.5 - - - +
159G LEU* 3.8 19.7 - - + -
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Residues in contact with VAL 77 (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 SER* 4.1 2.2 - - - +
76G LEU* 1.3 79.8 - - - +
78G THR* 1.3 71.8 + - - +
83G HIS* 4.0 14.4 - - + +
84G ARG 3.2 14.8 - - - +
85G PRO* 4.3 3.4 - - + -
86G HIS* 3.3 16.9 - - - +
140G PRO* 3.7 29.8 - - + -
141G PHE* 4.9 1.8 - - + -
157G VAL* 3.6 5.4 - - - +
158G ARG* 3.2 37.8 + - + +
160G CYS* 4.1 9.2 - - + -
179G LEU* 4.0 18.6 - - + -
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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