Contacts of the helix formed by residues 79 - 93 (chain P) in PDB entry 5LN3
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 GLU 79 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76P GLU 4.6 6.9 - - - +
77P ALA 4.9 1.0 - - - +
78P LYS* 1.3 88.4 - - - +
80P TRP* 1.4 98.3 + - + +
81P ASP* 3.4 15.5 - - - +
82P LEU* 3.5 11.1 + - + +
83P LEU* 3.1 23.0 + - - +
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Residues in contact with TRP 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P TYR* 3.4 47.3 - + - -
78P LYS 4.0 13.7 - - - -
79P GLU* 1.4 101.6 + - + +
81P ASP* 1.3 63.4 + - - +
83P LEU* 3.5 19.9 + - + +
84P ASN* 3.7 15.6 + - - +
112P VAL* 5.7 3.4 - - + -
114P GLU* 5.3 3.6 - - - -
117P ASP* 3.1 39.8 + - + -
120P ILE* 3.6 27.4 - - + +
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Residues in contact with ASP 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P GLU* 3.8 11.4 - - - +
80P TRP* 1.3 82.1 + - - +
82P LEU* 1.4 82.6 + - - +
84P ASN* 4.3 6.6 - - - +
85P GLU* 3.6 18.2 - - - +
120P ILE* 5.2 1.1 - - - +
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Residues in contact with LEU 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P ALA* 4.2 21.3 - - + +
39P ARG* 3.6 21.3 + - - +
78P LYS* 3.9 28.7 - - + -
79P GLU* 3.5 14.8 + - + +
80P TRP 3.4 0.4 - - - -
81P ASP* 1.4 91.6 - - - +
83P LEU* 1.3 58.5 + - - +
84P ASN 3.7 0.3 + - - -
85P GLU* 3.6 18.9 - - - +
86P ASN* 2.8 29.1 + - - +
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Residues in contact with LEU 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74P CYS* 4.0 11.2 - - - +
75P TYR* 3.2 66.2 - - + +
78P LYS* 4.2 12.3 - - + +
79P GLU 3.1 17.3 + - - +
80P TRP* 3.5 15.6 + - + +
82P LEU* 1.3 72.7 - - - +
84P ASN* 1.4 57.8 + - - +
86P ASN* 3.0 6.8 + - + +
87P ILE* 3.0 58.7 + - + +
108P CYS* 5.8 2.2 - - + -
112P VAL* 4.7 9.0 - - + -
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Residues in contact with ASN 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P TRP 3.7 13.6 + - - +
81P ASP* 4.3 7.0 - - - +
82P LEU 3.5 0.2 - - - -
83P LEU* 1.4 71.9 - - - +
85P GLU* 1.3 63.4 + - + +
87P ILE* 3.7 0.6 + - - -
88P MET* 3.5 21.7 + - - +
120P ILE* 3.6 20.4 - - - +
123P ARG* 4.6 8.9 - - - +
124P LEU* 3.6 54.2 - - - +
127P THR* 5.1 4.0 + - - -
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Residues in contact with GLU 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P ARG* 3.4 29.5 + - - +
81P ASP 3.6 12.0 - - - +
82P LEU* 3.6 24.9 - - - +
84P ASN* 1.3 77.1 - - + +
86P ASN* 1.4 61.1 + - - +
88P MET* 3.6 18.2 - - + +
89P LEU* 3.4 26.6 + - + +
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Residues in contact with ASN 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P GLY 5.2 1.2 + - - -
39P ARG* 3.1 31.5 + - - +
44P ILE* 5.5 6.9 - - - +
47P LEU* 5.3 12.1 - - + +
74P CYS* 5.9 4.9 - - + +
78P LYS* 4.2 25.0 - - + +
82P LEU 2.8 23.4 - - - +
83P LEU* 3.0 13.2 + - + +
85P GLU* 1.4 71.4 - - - +
87P ILE* 1.4 64.4 + - + +
89P LEU* 3.1 32.2 + - + +
90P LEU* 3.2 17.8 + - + +
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Residues in contact with ILE 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71P VAL* 5.5 2.2 - - + -
74P CYS* 4.5 10.1 - - - -
83P LEU* 3.0 44.5 + - + +
84P ASN* 3.7 0.4 + - - -
85P GLU 3.6 0.2 - - - -
86P ASN* 1.4 71.4 - - + +
88P MET* 1.3 65.9 + - - +
90P LEU* 3.3 30.2 + - + +
91P SER* 3.3 15.9 + - - +
105P VAL* 4.9 18.2 - - + -
108P CYS* 5.0 20.4 - - + -
124P LEU* 4.2 28.5 - - + -
128P LEU* 5.2 5.4 - - + -
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Residues in contact with MET 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P ASN 3.5 10.4 + - - +
85P GLU* 3.6 22.7 - - + +
86P ASN 3.3 0.2 - - - -
87P ILE* 1.3 77.7 - - - +
89P LEU* 1.4 63.9 + - + +
91P SER* 3.3 21.4 + - - -
92P LYS* 3.5 26.4 + - - +
124P LEU* 5.1 3.0 - - + +
127P THR* 3.6 31.9 - - + -
128P LEU* 6.4 1.6 - - - -
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Residues in contact with LEU 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P ARG* 5.3 8.1 - - - +
85P GLU* 3.4 18.2 - - + +
86P ASN* 3.1 24.9 + - - +
88P MET* 1.4 80.6 - - + +
90P LEU* 1.3 63.2 + - - +
92P LYS* 3.2 42.6 + - + +
93P ARG* 3.2 32.9 + - - +
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Residues in contact with LEU 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P LEU* 4.0 27.1 - - + -
51P GLU* 5.1 3.6 - - + +
67P LEU* 6.2 3.6 - - + -
70P VAL* 6.0 0.9 - - + -
71P VAL* 4.7 21.1 - - + -
74P CYS* 4.9 8.5 - - - -
86P ASN* 3.2 15.6 + - + +
87P ILE* 3.5 28.3 - - + +
89P LEU* 1.3 81.0 - - - +
91P SER* 1.4 55.7 + - - +
93P ARG* 3.0 56.3 + - + +
95P SER* 4.7 7.8 + - - +
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Residues in contact with SER 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P ILE* 3.3 13.8 + - - +
88P MET* 3.3 15.3 + - - -
90P LEU* 1.4 72.9 - - - +
92P LYS* 1.3 64.1 + - - +
93P ARG 3.2 9.5 + - - +
101P VAL* 6.3 2.5 - - - -
105P VAL* 5.3 7.1 - - - +
128P LEU* 4.7 16.0 - - - +
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Residues in contact with LYS 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P THR* 4.6 2.1 + - - -
88P MET* 3.8 27.7 + - - +
89P LEU* 3.3 40.5 - - + +
90P LEU 3.2 0.4 - - - -
91P SER* 1.3 78.7 - - - +
93P ARG* 1.3 66.3 + - + +
94P ARG 4.2 0.2 + - - -
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Residues in contact with ARG 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P LEU* 5.0 7.3 - - - +
51P GLU* 3.1 46.5 + - + +
56P THR* 3.7 17.9 - - - +
89P LEU* 3.2 40.7 + - - +
90P LEU* 3.0 50.9 + - - +
91P SER* 3.5 7.2 - - - +
92P LYS* 1.3 85.6 - - - +
94P ARG* 1.4 64.8 + - - +
95P SER* 3.7 17.2 + - - +
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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