Contacts of the helix formed by residues 99 - 116 (chain P) in PDB entry 3LUE
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 MET 99 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I ASP* 3.0 43.5 - - + +
341I ILE* 4.4 8.1 - - + -
98P LYS* 1.3 89.1 - - + +
100P ARG* 1.3 67.2 + - - +
101P PHE* 3.3 41.1 - - + -
102P HIS* 3.0 29.0 + - + +
103P LYS* 3.2 11.5 + - - +
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Residues in contact with ARG 100 (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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47G MET 3.8 0.2 - - - -
48G GLY* 2.4 50.4 - - - +
144I ALA 5.9 2.9 - - - +
145I SER 4.4 2.5 - - - -
146I GLY* 3.8 30.8 + - - -
148I THR* 4.3 0.4 - - - +
98P LYS 3.9 0.2 + - - -
99P MET* 1.3 72.5 - - - +
101P PHE* 1.3 68.6 + - + +
103P LYS* 3.0 14.6 + - - +
104P ILE* 3.0 28.2 + - + +
127P GLU* 3.9 15.4 + - - +
130P VAL* 4.3 15.6 - - + +
131P ASP* 2.6 41.2 + - - -
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Residues in contact with PHE 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLN* 5.5 0.6 - - - +
23I GLY* 5.8 2.0 - - - -
24I ASP 5.3 4.0 - - - -
25I ASP* 4.7 1.1 - - - -
143I TYR* 4.9 6.5 - - + +
144I ALA 4.9 7.4 - - - -
341I ILE* 3.8 14.6 - - + -
344I SER* 5.6 2.7 - - - -
345I ILE* 1.9 72.5 - - + -
348I SER* 5.4 0.4 - - - -
349I LEU* 4.4 4.2 - - - +
99P MET* 3.3 40.8 - - + -
100P ARG* 1.3 81.2 - - + +
102P HIS* 1.3 102.0 + + - +
104P ILE* 3.5 12.9 + - + +
105P ALA* 3.0 23.4 + - - +
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Residues in contact with HIS 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLY* 4.3 24.4 + - - -
25I ASP* 4.7 2.8 + - - -
348I SER* 5.2 5.6 + - - -
95P ASP* 4.5 18.5 + - + +
96P LYS 3.4 19.4 + - - +
97P GLY* 3.5 31.1 - - - +
99P MET* 3.0 46.5 + - + +
101P PHE* 1.3 99.1 - + - +
103P LYS* 1.3 58.7 + - + +
105P ALA* 3.4 6.3 + - - +
106P ASN* 3.0 35.2 + - - +
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Residues in contact with LYS 103 (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 ARG* 3.7 48.8 - - + +
75P ASN* 3.7 33.1 - - + +
98P LYS* 3.6 25.2 + - - +
99P MET 3.5 10.3 - - - +
100P ARG* 3.0 11.5 + - - +
102P HIS* 1.3 75.5 - - + +
104P ILE* 1.3 60.4 + - - +
106P ASN* 3.2 1.4 + - - +
107P VAL* 2.8 34.7 + - - +
130P VAL* 3.8 19.4 + - + -
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Residues in contact with ILE 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G GLY* 2.9 21.1 - - - -
49G GLN* 1.6 82.8 - - + +
50G LYS* 4.5 1.6 - - + -
349I LEU* 6.3 0.7 - - + -
100P ARG* 3.0 24.4 + - + +
101P PHE* 3.7 11.0 - - - +
103P LYS* 1.3 74.3 - - - +
105P ALA* 1.3 59.5 + - - +
107P VAL 3.8 0.5 - - - -
108P ASN* 2.9 41.1 + - - +
126P ALA* 3.9 10.3 - - + +
127P GLU* 5.1 2.7 - - - -
130P VAL* 3.7 20.4 - - + -
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Residues in contact with ALA 105 (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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349I LEU* 3.1 36.1 - - + +
95P ASP* 4.2 17.9 - - - +
101P PHE 3.0 12.3 + - - +
102P HIS* 3.6 5.6 - - - +
103P LYS 3.2 0.2 - - - -
104P ILE* 1.3 78.5 - - - +
106P ASN* 1.3 62.1 + - - +
108P ASN* 3.3 7.7 + - - +
109P LYS* 3.1 28.7 + - - +
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Residues in contact with ASN 106 (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 ASN 3.7 18.1 + - - +
76P GLY* 4.6 3.6 - - - -
77P LEU* 4.1 13.7 - - + +
80P MET* 3.5 16.4 - - - +
94P PRO* 3.2 9.5 - - - +
95P ASP* 2.7 48.3 + - - +
97P GLY 5.3 1.6 + - - -
102P HIS* 3.0 23.2 + - - +
105P ALA* 1.3 74.6 - - - +
107P VAL* 1.3 64.8 + - - +
109P LYS* 3.0 30.8 + - - +
110P ALA 3.3 8.0 + - - -
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Residues in contact with VAL 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P ARG 3.8 15.5 - - - +
76P GLY* 3.7 24.0 - - - +
79P LEU* 4.7 4.7 - - + -
103P LYS 2.8 23.6 + - - +
104P ILE 4.0 2.7 - - - +
106P ASN* 1.3 73.1 - - - +
108P ASN* 1.3 56.9 + - - +
110P ALA* 3.3 6.4 + - - +
111P LEU* 2.9 35.6 + - + +
126P ALA* 3.5 29.6 - - + -
129P ILE* 3.7 28.9 - - + -
130P VAL* 4.1 5.2 - - + -
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Residues in contact with ASN 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLN* 4.2 11.4 + - - +
51G ASP* 4.4 16.6 + - - +
52G SER* 5.4 2.6 + - - +
104P ILE* 2.9 33.9 + - - +
105P ALA* 3.6 8.2 - - - +
106P ASN 3.1 0.2 - - - -
107P VAL* 1.3 75.8 - - - +
109P LYS* 1.3 58.8 + - - +
111P LEU* 3.8 14.0 - - - +
112P ASP* 2.9 46.5 + - - +
126P ALA* 3.0 23.4 - - - +
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Residues in contact with LYS 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350I SER* 4.9 17.2 + - - +
80P MET* 3.8 20.0 - - + -
91P LEU* 4.4 3.3 - - - +
92P PRO* 4.4 27.3 - - + +
93P ARG 3.4 22.7 + - - +
95P ASP* 3.2 23.9 + - - -
105P ALA* 3.1 16.9 + - - +
106P ASN* 3.0 35.3 + - - +
108P ASN* 1.3 77.0 - - - +
110P ALA* 1.3 58.3 + - - +
112P ASP* 3.6 5.0 + - - +
113P PHE* 3.0 28.5 + - - +
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Residues in contact with ALA 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P LEU* 3.7 26.7 - - + -
80P MET* 4.1 13.8 - - + +
83P LEU* 3.6 25.5 - - + +
91P LEU* 4.2 5.2 - - - -
106P ASN 3.3 3.3 + - - +
107P VAL 3.5 8.1 - - - +
108P ASN 3.2 0.2 - - - -
109P LYS* 1.3 77.9 - - - +
111P LEU* 1.3 66.4 + - - +
113P PHE* 3.0 4.0 + - - +
114P ILE* 3.0 27.5 + - + +
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Residues in contact with LEU 111 (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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52G SER* 4.2 3.6 - - - +
79P LEU* 5.4 0.7 - - + -
107P VAL* 2.9 25.9 + - + +
108P ASN* 3.8 15.3 - - - +
110P ALA* 1.3 73.3 - - - +
112P ASP* 1.3 60.7 + - - +
114P ILE* 3.4 7.8 + - + +
115P ALA* 2.9 29.0 + - - +
121P LEU* 3.7 20.8 - - + +
124P ILE* 4.1 23.1 - - + +
125P GLY 3.8 5.6 - - - +
126P ALA* 3.4 37.5 - - - +
129P ILE* 4.7 1.6 - - + -
140P MET* 3.8 29.8 - - + -
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Residues in contact with ASP 112 (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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108P ASN* 2.9 33.7 + - - +
109P LYS* 3.9 4.5 - - - +
111P LEU* 1.3 75.9 - - - +
113P PHE* 1.3 60.9 + - - +
115P ALA* 3.2 7.7 + - - +
116P SER* 2.8 31.5 + - - -
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Residues in contact with PHE 113 (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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83P LEU* 4.1 21.8 - - + -
87P SER* 3.7 21.3 - - - -
89P GLU* 3.8 21.3 - - + -
90P ARG 5.1 3.6 - - - -
91P LEU* 3.6 39.3 - - + -
92P PRO* 5.7 2.5 - - + -
109P LYS 3.0 15.8 + - - +
110P ALA 3.0 7.6 + - - +
112P ASP* 1.3 76.7 - - - +
114P ILE* 1.3 63.4 + - - +
116P SER* 2.5 27.8 + - - -
117P LYS* 3.4 28.8 + - - +
148P PHE* 3.7 23.8 - + - -
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Residues in contact with ILE 114 (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 LEU* 5.6 0.2 - - + -
83P LEU* 4.0 22.0 - - + -
110P ALA* 3.0 22.7 + - + +
111P LEU* 3.5 13.5 - - + +
113P PHE* 1.3 75.2 - - - +
115P ALA* 1.3 61.0 + - - +
117P LYS* 2.9 26.4 + - - +
119P VAL* 3.2 45.9 - - + +
121P LEU* 4.0 9.9 - - + -
140P MET* 4.5 14.6 - - + +
143P THR* 4.4 6.3 - - + +
144P ILE* 3.4 34.1 - - + -
148P PHE* 4.6 6.3 - - + -
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Residues in contact with ALA 115 (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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68G LYS* 5.1 10.1 - - + -
111P LEU 2.9 13.2 + - - +
112P ASP* 3.6 9.9 - - - +
114P ILE* 1.3 75.6 - - - +
116P SER* 1.3 61.8 + - - +
117P LYS 3.1 1.4 + - - -
118P GLY* 3.1 11.4 + - - -
119P VAL 3.2 21.2 + - - +
121P LEU* 3.4 20.6 - - + -
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Residues in contact with SER 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P ASP 2.8 13.2 + - - -
113P PHE* 2.5 30.4 + - - -
115P ALA* 1.3 75.8 - - - +
117P LYS* 1.3 63.4 + - - +
118P GLY 3.1 4.2 + - - -
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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
------------------------------------------------------------
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