Contacts of the helix formed by residues 68 - 77 (chain G) in PDB entry 4GEK
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 GLY 68 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ASP* 4.4 1.6 - - - -
65G CYS* 2.9 13.2 + - - -
66G SER 3.2 1.8 + - - -
67G LEU* 1.3 80.8 - - - +
69G ALA* 1.3 59.7 + - - +
70G ALA 3.3 3.1 - - - -
71G THR* 3.2 15.0 + - - -
72G LEU* 2.8 37.7 + - - +
98G CYS* 3.8 12.5 - - - -
102G ILE* 4.5 3.4 - - - -
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Residues in contact with ALA 69 (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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39G TYR* 3.1 29.4 - - + +
43G ILE* 4.0 13.6 - - + +
65G CYS 4.1 3.0 + - - -
67G LEU* 3.5 4.3 - - + +
68G GLY* 1.3 77.1 - - - +
70G ALA* 1.4 61.9 + - - +
72G LEU* 3.4 2.1 + - - +
73G SER* 3.1 23.2 + - - -
76G ARG* 5.0 1.4 + - - -
302G SO4 3.7 21.7 + - - +
303G GEK 3.7 6.2 + - - +
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Residues in contact with ALA 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ILE* 3.9 13.8 - - + +
46G ILE* 4.3 8.0 - - + +
62G ASP* 3.7 21.0 + - - +
68G GLY 3.3 0.4 - - - -
69G ALA* 1.4 75.4 - - - +
71G THR* 1.3 67.1 + - - +
73G SER* 3.2 5.4 + - - -
74G VAL* 2.9 28.3 + - - +
130G VAL* 3.9 22.4 - - + -
132G ASN* 4.6 0.4 - - + -
303G GEK 4.1 16.0 + - - +
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Residues in contact with THR 71 (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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62G ASP* 2.7 39.7 + - - +
65G CYS* 4.5 0.2 - - - +
68G GLY* 3.4 12.6 - - - -
70G ALA* 1.3 76.4 - - - +
72G LEU* 1.3 61.7 + - + +
74G VAL* 3.3 7.0 + - - +
75G ARG* 2.8 27.3 + - - +
85G ILE* 3.7 22.5 - - + +
87G ALA* 3.6 10.7 - - - +
102G ILE* 3.9 23.3 - - + -
111G VAL* 4.0 16.4 - - + -
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G GLY 2.8 22.8 + - - +
69G ALA 4.0 2.0 - - - +
71G THR* 1.3 70.9 - - + +
73G SER* 1.3 60.6 + - - +
75G ARG* 3.6 31.7 - - - +
76G ARG* 3.0 53.0 + - + +
101G HIS* 3.6 35.0 - - + +
102G ILE* 4.1 22.0 - - + -
105G TYR* 4.4 22.9 - - + -
302G SO4 3.8 15.7 - - - +
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Residues in contact with SER 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ILE* 2.7 41.1 + - - +
44G SER* 4.5 1.7 - - - -
46G ILE* 4.7 1.6 - - - -
47G GLY* 3.3 13.6 + - - -
69G ALA 3.1 16.8 + - - -
70G ALA* 3.2 6.3 + - - -
72G LEU* 1.3 75.4 - - - +
74G VAL* 1.3 63.5 + - - +
76G ARG* 3.5 17.9 + - - +
77G ASN* 2.8 29.3 + - - +
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Residues in contact with VAL 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ILE* 3.6 21.5 - - + -
47G GLY* 4.6 0.6 - - - -
50G ALA* 4.0 18.6 - - + +
54G VAL* 4.3 0.4 - - + -
60G VAL* 4.0 26.7 - - + -
70G ALA 2.9 19.1 + - - +
71G THR* 3.5 8.7 - - - +
73G SER* 1.3 76.0 - - - +
75G ARG* 1.3 57.8 + - - +
77G ASN* 2.9 19.9 + - - +
78G ILE* 3.2 31.1 + - + +
85G ILE* 3.9 9.6 - - + -
128G MET* 4.2 13.0 - - + -
130G VAL* 4.6 4.9 - - + -
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Residues in contact with ARG 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G THR* 2.8 20.4 + - - +
72G LEU* 3.2 26.8 + - + +
74G VAL* 1.3 71.9 - - - +
76G ARG* 1.3 63.0 + - + +
77G ASN 3.1 0.9 + - - -
78G ILE* 3.4 21.1 + - - +
85G ILE* 3.6 14.4 - - + -
102G ILE* 3.9 19.7 + - - +
105G TYR* 2.9 34.5 + - - +
106G LYS* 4.7 0.4 + - - +
107G ALA* 3.6 41.8 + - + +
108G PRO* 5.9 0.5 - - - +
109G THR* 2.8 34.5 + - - +
110G PRO* 5.1 2.8 - - - +
111G VAL* 3.7 20.0 - - - +
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Residues in contact with ARG 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ILE* 4.7 7.9 - - - +
69G ALA 5.0 0.6 + - - -
72G LEU* 3.0 40.3 + - + +
73G SER* 3.5 28.4 + - - +
74G VAL 3.2 0.4 - - - -
75G ARG* 1.3 77.3 - - + +
77G ASN* 1.3 65.2 + - - +
78G ILE 3.6 0.7 - - - -
79G HIS* 3.6 16.6 - - - -
105G TYR* 6.3 1.8 - - - -
302G SO4 3.0 27.2 + - - -
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Residues in contact with ASN 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLY* 3.1 37.7 - - - +
48G MET* 4.7 1.7 + - - +
50G ALA* 4.1 2.5 - - + +
51G GLU* 3.0 47.9 + - - +
73G SER* 2.8 22.9 + - - +
74G VAL 2.9 10.5 + - - +
76G ARG* 1.3 84.9 - - - +
78G ILE* 1.3 61.6 + - - +
79G HIS* 3.7 11.1 - - - -
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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
------------------------------------------------------------
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