Contacts of the helix formed by residues 100 - 120 (chain H) in PDB entry 4QLC
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 PRO 100 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ARG* 5.5 3.6 - - - +
91G GLU* 3.1 18.1 - - - +
94G LYS* 3.6 35.2 - - + +
95G LEU* 4.1 35.9 - - + +
98H LEU 3.6 8.1 - - - +
99H LEU* 1.3 87.7 - - + +
101H GLY* 1.3 68.8 + - - +
103H LEU* 3.2 20.1 + - + +
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Residues in contact with GLY 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ARG* 4.7 13.3 - - - +
91G GLU* 3.9 6.9 + - - -
94G LYS* 5.7 0.8 - - - +
99H LEU 3.9 1.8 + - - -
100H PRO* 1.3 72.3 - - - +
102H GLU* 1.3 64.5 + - - -
104H ALA* 3.2 17.2 + - - +
105H LYS* 3.5 15.1 + - - +
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Residues in contact with GLU 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G TYR* 5.5 0.2 - - - -
91G GLU* 3.5 21.5 + - + +
100H PRO 3.4 0.6 + - - -
101H GLY* 1.3 71.8 - - - -
103H LEU* 1.3 63.6 + - - +
105H LYS* 3.1 27.5 + - - +
106H HIS* 3.0 59.0 + - + -
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Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G TYR* 3.9 23.4 - - + +
57G LEU* 3.8 21.3 - - + -
60G GLU* 4.4 15.0 - - + -
89G ASP* 5.6 0.4 - - - +
91G GLU* 3.2 48.1 + - + +
92G LEU* 4.1 7.9 - - + +
95G LEU* 3.9 25.6 - - + -
99H LEU* 4.2 10.7 - - + +
100H PRO* 3.2 14.0 + - + +
102H GLU* 1.3 78.3 - - - +
104H ALA* 1.3 57.0 + - - +
106H HIS 3.5 0.2 + - - -
107H ALA* 3.0 30.4 + - - +
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H VAL* 4.2 10.1 - - + +
96H ARG* 4.6 16.6 - - - +
99H LEU* 3.3 35.3 - - + +
100H PRO 3.6 0.6 + - - -
101H GLY 3.2 9.9 + - - +
103H LEU* 1.3 75.4 - - - +
105H LYS* 1.3 63.2 + - + +
107H ALA* 3.1 5.6 + - - +
108H VAL* 2.8 36.0 + - - +
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Residues in contact with LYS 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ARG* 5.6 5.1 - - - +
101H GLY* 3.5 15.2 + - - +
102H GLU* 3.1 32.0 + - - +
104H ALA* 1.3 77.7 - - + +
106H HIS* 1.3 61.0 + - + +
108H VAL* 3.3 7.5 + - - +
109H SER* 3.0 25.9 + - - -
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Residues in contact with HIS 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G TYR* 3.3 36.0 + + + +
201G CIT 5.0 9.6 - - + -
102H GLU* 3.0 60.6 + - + +
105H LYS* 1.3 75.0 - - + +
107H ALA* 1.3 60.5 + - - +
109H SER* 2.4 27.7 + - - +
110H GLU* 2.9 19.6 + - + +
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Residues in contact with ALA 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G VAL* 3.5 37.5 - - + +
56G TYR* 4.2 15.1 - - + -
95H VAL* 4.0 6.5 - - + -
99H LEU* 3.9 13.9 - - + -
103H LEU 3.0 19.7 + - - +
104H ALA 3.1 4.5 + - - +
106H HIS* 1.3 78.0 - - - +
108H VAL* 1.3 56.3 + - - +
110H GLU* 3.9 2.9 - - - +
111H GLY* 2.9 22.5 + - - -
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Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G TYR* 3.2 22.1 + - - +
92H GLN* 4.4 11.7 - - + +
95H VAL* 4.2 13.5 - - + -
96H ARG* 3.4 46.2 - - + +
104H ALA 2.8 21.4 + - - +
105H LYS* 3.6 5.4 - - - +
106H HIS 3.2 0.2 - - - -
107H ALA* 1.3 73.3 - - - +
109H SER* 1.3 61.5 + - - +
112H THR* 2.8 42.9 + - - +
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Residues in contact with SER 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H LYS 3.0 13.2 + - - -
106H HIS* 2.4 33.6 + - - +
108H VAL* 1.3 77.5 - - - +
110H GLU* 1.3 66.5 + - - +
112H THR* 3.8 4.7 - - - -
113H LYS* 2.9 31.0 + - - +
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Residues in contact with GLU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ALA* 3.7 18.9 - - + +
56G TYR* 3.9 30.1 - - + -
201G CIT 4.4 23.2 - - - +
106H HIS* 2.9 17.3 + - + +
107H ALA 3.9 3.8 - - - +
109H SER* 1.3 82.4 + - - +
111H GLY* 1.3 66.5 + - - +
113H LYS* 3.4 34.3 + - - +
114H ALA* 3.1 24.9 + - - +
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Residues in contact with GLY 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G TYR* 3.7 33.6 - - - -
52G ALA* 3.8 12.7 - - - +
53G VAL* 4.5 0.4 - - - +
107H ALA 2.9 18.5 + - - -
110H GLU* 1.3 77.4 - - - +
112H THR* 1.3 62.5 + - - +
114H ALA* 3.4 2.1 + - - +
115H VAL* 3.2 22.5 + - - +
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Residues in contact with THR 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G TYR* 3.7 12.7 + - - -
92H GLN* 5.1 1.9 + - - -
108H VAL* 2.8 27.6 + - - +
109H SER* 3.8 4.9 - - - -
111H GLY* 1.3 72.3 - - - +
113H LYS* 1.3 67.7 + - - +
115H VAL* 3.0 25.4 - - + +
116H THR* 3.1 26.5 + - + +
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Residues in contact with LYS 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ALA 6.1 0.2 - - - +
201G CIT 5.9 0.6 + - - -
109H SER 2.9 17.6 + - - +
110H GLU* 3.5 33.9 + - - +
111H GLY 3.3 0.2 - - - -
112H THR* 1.3 76.0 - - - +
114H ALA* 1.3 63.2 + - + +
116H THR* 2.4 25.8 + - - -
117H LYS* 3.2 27.5 + - + +
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Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ALA* 3.7 24.7 - - - +
22G LEU* 4.0 9.9 - - + -
48G VAL* 3.7 13.7 - - + -
52G ALA* 3.6 30.3 - - + -
110H GLU 3.1 4.8 + - - +
111H GLY 3.9 0.9 - - - +
113H LYS* 1.3 81.8 - - + +
115H VAL* 1.3 62.7 + - - +
117H LYS* 3.3 2.2 + - - +
118H TYR* 3.0 24.8 + - - +
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Residues in contact with VAL 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G GLY* 4.0 30.1 - - - +
48G VAL* 3.6 13.3 - - + +
49G TYR* 4.4 11.0 - - + -
88H SER* 4.2 9.2 - - - +
111H GLY 3.2 12.1 + - - +
112H THR* 3.0 28.7 - - + +
114H ALA* 1.3 77.8 - - - +
116H THR* 1.3 66.5 + - + +
118H TYR* 3.4 4.1 + - + +
119H THR* 3.1 39.8 + - + +
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Residues in contact with THR 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H THR* 3.1 25.3 + - + +
113H LYS* 2.4 31.7 + - - -
115H VAL* 1.3 81.7 - - + +
117H LYS* 1.3 62.7 + - - +
119H THR* 2.5 23.9 + - - -
120H SER* 3.3 9.5 + - - -
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Residues in contact with LYS 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ASN 5.2 1.6 + - - -
19G ARG 3.4 18.3 + - - +
20G ALA 4.2 12.6 - - - +
21G GLY* 4.9 10.7 - - - +
113H LYS* 3.2 31.9 + - + +
114H ALA 3.8 4.5 - - - +
116H THR* 1.3 84.3 + - - +
118H TYR* 1.3 60.8 + - - +
120H SER* 2.5 26.2 + - - -
121H SER* 3.8 5.2 + - - -
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Residues in contact with TYR 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ARG* 3.4 64.0 + - + +
19G ARG* 3.3 56.8 + - + -
20G ALA* 3.8 8.5 - - + -
26G VAL* 5.2 0.6 - - + +
44G ALA* 4.1 23.7 + - + +
45G GLY* 5.6 2.0 - - - -
48G VAL* 3.8 29.6 - - + -
114H ALA 3.0 17.3 + - - +
115H VAL* 3.7 5.6 - - - +
117H LYS* 1.3 76.7 - - - +
119H THR* 1.3 68.7 + - + +
120H SER 3.4 0.3 + - - -
121H SER* 3.5 5.5 + - - -
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Residues in contact with THR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G GLY* 6.2 0.9 - - - -
115H VAL* 3.1 26.6 + - + +
116H THR* 2.5 26.4 + - - -
118H TYR* 1.3 78.8 - - + +
120H SER* 1.3 57.2 + - - +
121H SER 3.1 13.2 + - - -
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Residues in contact with SER 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H THR 3.3 9.4 + - - -
117H LYS* 2.5 26.2 + - - -
119H THR* 1.3 75.6 + - - +
121H SER* 1.3 59.9 + - - +
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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
------------------------------------------------------------
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