Contacts of the helix formed by residues 68 - 77 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASP* 4.2 2.0 - - - -
65A CYS* 2.8 13.6 + - - -
66A SER 3.2 1.8 + - - -
67A LEU* 1.3 80.8 - - - +
69A ALA* 1.3 66.9 + - - +
70A ALA 3.3 2.2 - - - -
71A THR* 3.2 15.9 + - - -
72A LEU* 2.8 30.8 + - - +
98A CYS* 3.9 11.7 - - - -
102A ILE* 4.4 3.1 - - - -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 3.1 29.2 - - + +
43A ILE* 4.0 13.6 - - + +
65A CYS 4.1 3.2 + - - -
67A LEU* 3.6 3.5 - - + +
68A GLY* 1.3 78.2 - - - +
70A ALA* 1.3 63.2 + - - +
72A LEU* 4.0 1.7 - - - +
73A SER* 3.1 22.7 + - - -
76A ARG* 5.0 0.5 + - - -
301A SO4 3.5 23.1 + - - +
302A GEK 3.8 5.8 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.9 12.8 - - + +
46A ILE* 4.3 10.0 - - + +
62A ASP* 3.7 20.5 + - - +
68A GLY 3.3 0.4 - - - -
69A ALA* 1.3 75.6 - - - +
71A THR* 1.3 68.0 + - - +
73A SER* 3.2 4.5 + - - -
74A VAL* 2.9 29.4 + - - +
130A VAL* 3.9 22.9 - - + -
132A ASN* 4.5 0.4 - - + -
302A GEK 4.1 16.0 + - - +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASP* 2.7 38.4 + - - +
68A GLY* 3.4 13.0 - - - -
70A ALA* 1.3 74.9 - - - +
72A LEU* 1.3 60.2 + - - +
74A VAL* 3.3 7.1 + - - +
75A ARG* 2.8 28.7 + - - +
85A ILE* 3.7 23.5 - - + +
87A ALA* 3.6 10.7 - - - +
102A ILE* 3.7 23.6 - - + -
111A VAL* 4.0 16.6 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLY 2.8 19.7 + - - +
69A ALA 4.0 1.6 - - - +
71A THR* 1.3 74.1 - - - +
73A SER* 1.3 57.9 + - - +
75A ARG* 3.7 31.0 - - - +
76A ARG* 3.0 52.8 + - + +
101A HIS* 3.5 35.9 - - + +
102A ILE* 4.0 24.0 - - + -
105A TYR* 4.3 22.7 - - + -
301A SO4 3.7 18.4 - - - +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 2.7 41.2 + - - +
44A SER* 4.6 1.6 - - - -
46A ILE* 4.7 1.6 - - - -
47A GLY* 3.3 13.2 + - - -
69A ALA 3.1 16.8 + - - -
70A ALA* 3.2 5.8 + - - -
72A LEU* 1.3 76.4 - - - +
74A VAL* 1.3 64.1 + - - +
76A ARG* 3.5 18.4 + - - +
77A ASN* 2.8 30.0 + - - +
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.6 21.1 - - + -
47A GLY* 4.6 0.6 - - - -
50A ALA* 3.9 18.3 - - + +
54A VAL* 4.3 0.9 - - + -
60A VAL* 4.0 28.9 - - + -
70A ALA 2.9 18.0 + - - +
71A THR* 3.6 8.5 - - - +
73A SER* 1.3 75.9 - - - +
75A ARG* 1.3 59.1 + - - +
77A ASN* 2.8 20.3 + - - +
78A ILE* 3.3 30.9 + - + +
85A ILE* 4.1 6.7 - - + -
128A MET* 4.0 14.6 - - + -
130A VAL* 4.5 5.2 - - + -
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 2.8 20.1 + - - +
72A LEU* 3.2 26.4 + - + +
74A VAL* 1.3 73.7 - - - +
76A ARG* 1.3 61.7 + - + +
77A ASN 3.1 1.0 + - - -
78A ILE* 3.3 21.3 + - - +
85A ILE* 3.5 15.7 - - + -
99A ARG* 5.7 1.0 - - - +
102A ILE* 4.0 19.5 + - - +
105A TYR* 3.0 33.9 + - - +
106A LYS 4.6 0.2 + - - -
107A ALA* 3.6 41.8 + - + +
109A THR* 2.9 34.4 + - - +
110A PRO* 5.0 2.4 - - - +
111A VAL* 3.7 20.1 - - - +
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 4.6 8.3 - - - +
69A ALA 5.0 0.6 + - - -
72A LEU* 3.0 39.9 + - + +
73A SER* 3.5 28.2 + - - +
74A VAL 3.3 0.2 - - - -
75A ARG* 1.3 76.7 - - + +
77A ASN* 1.4 65.7 + - - +
78A ILE 3.6 0.8 - - - +
79A HIS* 3.7 16.6 + - - -
105A TYR* 6.3 1.6 - - - -
301A SO4 3.1 26.0 + - - -
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLY* 3.2 35.9 - - - +
48A MET* 5.1 1.2 - - - -
50A ALA* 4.1 4.3 - - + +
51A GLU* 3.0 49.2 + - - +
73A SER* 2.8 23.8 + - - +
74A VAL 2.8 11.3 + - - +
76A ARG* 1.4 86.5 - - - +
78A ILE* 1.3 58.8 + - - +
79A HIS* 3.7 10.2 + - - -
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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