Contacts of the helix formed by residues 108 - 127 (chain H) in PDB entry 2GTL
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 108 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H LEU 3.0 9.1 - - - +
107H LYS* 1.3 83.3 - - + +
109H GLU* 1.3 62.4 + - + +
110H PHE 3.2 1.0 + - - -
111H PHE* 3.6 11.9 + - + +
112H ASP* 3.8 7.2 + - - -
147H LYS* 3.5 52.9 - - + +
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Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H GLU* 5.1 6.2 - - - +
107H LYS* 2.7 33.5 + - + +
108H PRO* 1.3 77.5 - - + +
110H PHE* 1.3 67.6 + - + +
111H PHE 3.2 0.2 - - - -
112H ASP* 3.0 17.6 + - + +
113H ILE* 3.0 31.7 + - + +
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Residues in contact with PHE 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H GLU* 4.0 34.5 - - + -
49H ILE* 3.7 27.9 - - + +
52H PRO* 5.1 6.3 - - + -
105H ASN 4.4 8.3 - - - -
106H LEU* 4.2 6.5 - - + -
107H LYS* 2.7 58.3 + - + +
109H GLU* 1.3 75.8 - - + +
111H PHE* 1.3 65.3 + - + +
113H ILE* 3.0 22.5 - - + +
114H PHE* 2.8 26.0 + - - +
160H HEM 3.5 35.3 - - + +
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Residues in contact with PHE 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H HIS* 3.6 27.4 - + + -
106H LEU* 4.5 18.2 - - + -
107H LYS 4.4 2.7 - - - -
108H PRO* 3.9 12.8 - - + +
109H GLU 3.2 0.4 - - - -
110H PHE* 1.3 80.0 - - + +
112H ASP* 1.3 66.0 + - - +
113H ILE 2.9 1.6 - - - -
114H PHE* 3.4 3.1 - - - +
115H LEU 2.8 21.7 + - - -
143H ILE* 3.3 39.5 - - + +
146H ILE* 3.4 38.4 - - + -
147H LYS* 4.1 17.5 - - + -
160H HEM 3.6 44.0 - + + -
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Residues in contact with ASP 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H PRO 4.2 6.3 - - - +
109H GLU* 3.0 18.5 + - + +
111H PHE* 1.3 78.4 - - - +
113H ILE* 1.3 61.7 + - + +
115H LEU* 3.8 10.5 + - - +
116H LYS* 3.2 20.7 + - - +
140H ASP* 5.6 1.6 - - - +
143H ILE* 4.8 3.4 - - - +
147H LYS* 3.2 30.7 + - - +
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Residues in contact with ILE 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ILE* 4.8 12.8 - - + -
45H ASP* 4.7 0.2 - - - +
46H HIS* 3.4 48.9 - - + +
48H GLU* 5.2 1.1 - - - +
49H ILE* 4.8 2.2 - - + -
109H GLU* 3.0 23.8 - - + +
110H PHE* 3.0 30.3 - - + +
112H ASP* 1.3 75.5 - - + +
114H PHE* 1.3 69.4 + - - +
115H LEU 3.1 1.6 - - - -
116H LYS* 2.8 24.6 + - - +
117H HIS* 3.1 32.0 + - + +
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Residues in contact with PHE 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LEU* 3.9 24.7 - - + -
39H TRP* 3.7 31.0 - + + -
42H ILE* 3.7 26.1 - - + +
73H VAL* 4.6 7.6 - - + -
74H LEU* 5.8 1.1 - - + -
77H LEU* 4.4 13.0 - - + -
110H PHE 2.8 15.8 + - - +
111H PHE* 3.4 8.1 - - - +
113H ILE* 1.3 73.5 - - - +
115H LEU* 1.3 63.9 + - - +
117H HIS* 3.2 2.9 + - - +
118H LEU* 2.9 48.2 + - + +
139H VAL* 5.8 0.4 - - + -
143H ILE* 4.7 3.6 - - + -
160H HEM 3.3 57.2 - - + -
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H PHE 2.8 10.0 + - - +
112H ASP* 3.8 9.9 - - - +
114H PHE* 1.3 78.8 - - - +
116H LYS* 1.3 68.9 + - - +
118H LEU* 3.2 5.0 + - + -
119H LEU* 3.1 44.4 + - + +
136H HIS* 4.2 19.1 - - + +
139H VAL* 3.3 35.9 - - + -
140H ASP* 4.0 28.9 - - + +
143H ILE* 3.2 23.8 - - + -
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Residues in contact with LYS 116 (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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44D ASP* 5.7 11.0 - - - +
45H ASP* 3.3 26.1 + - - -
46H HIS* 4.4 7.5 + - - -
112H ASP 3.2 10.6 + - - +
113H ILE* 2.8 23.2 + - - +
115H LEU* 1.3 76.4 - - - +
117H HIS* 1.3 71.7 + - + +
119H LEU* 3.5 8.1 + - - +
120H HIS* 3.1 22.8 + - + +
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Residues in contact with HIS 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LEU* 3.7 9.9 - - + +
41H ASP* 3.2 45.2 + - + +
42H ILE* 3.6 25.6 - - + +
45H ASP* 3.8 32.0 - - + +
113H ILE* 3.1 25.7 + - + +
114H PHE 3.8 1.8 - - - +
116H LYS* 1.3 88.8 - - + +
118H LEU* 1.3 68.1 + - - +
119H LEU 2.9 1.8 - - - -
120H HIS* 2.7 15.3 + + + +
121H VAL* 2.7 27.3 + - + +
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Residues in contact with LEU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H TRP* 4.4 2.5 - - + -
34H PHE* 3.9 29.4 - - + -
38H LEU* 3.7 16.6 - - + +
77H LEU* 3.5 33.9 - - + -
114H PHE* 2.9 34.5 + - + +
115H LEU* 3.7 6.7 - - + +
117H HIS* 1.3 72.9 - - - +
119H LEU* 1.3 58.7 + - + +
121H VAL* 3.9 0.6 - - - +
122H LEU* 3.0 45.7 + - + +
135H TRP* 4.9 3.6 - - + -
139H VAL* 4.2 30.1 - - + -
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Residues in contact with LEU 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D TYR* 4.7 0.5 + - - -
115H LEU* 3.1 38.7 + - + +
116H LYS* 3.6 6.3 - - - +
117H HIS 2.9 0.8 - - - -
118H LEU* 1.3 74.6 - - + +
120H HIS* 1.3 61.2 + - - +
122H LEU* 3.3 0.6 + - + -
123H GLY* 2.8 28.8 + - - -
130H PHE* 3.6 23.3 - - + -
132H PHE* 4.2 24.2 - - + +
135H TRP* 3.6 38.1 - - + -
136H HIS* 3.8 30.7 - - + +
139H VAL* 5.1 0.7 - - + -
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Residues in contact with HIS 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ARG* 3.6 41.7 + - + +
41D ASP* 5.1 6.5 - - - -
44D ASP* 3.5 23.8 + - - +
62D TYR* 5.5 0.4 - - - -
41H ASP* 3.9 21.7 + - - -
116H LYS* 3.1 14.8 + - + +
117H HIS* 2.7 24.4 + + + +
119H LEU* 1.3 72.3 - - - +
121H VAL* 1.3 67.9 + - + +
123H GLY* 3.2 10.7 + - - -
124H ASP* 3.3 20.8 + - - +
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Residues in contact with VAL 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H PHE* 3.7 37.5 - - + +
37H GLU* 4.0 25.6 - - + +
38H LEU* 4.0 29.2 - - + +
41H ASP* 5.3 5.4 - - - +
117H HIS* 2.7 23.7 + - + +
118H LEU 3.9 4.0 - - - +
120H HIS* 1.3 76.0 - - + +
122H LEU* 1.3 66.7 + - - +
123H GLY 2.9 1.3 - - - -
124H ASP* 2.8 19.2 + - - +
125H ARG* 3.0 17.3 + - + +
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Residues in contact with LEU 122 (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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21H TRP* 3.9 9.6 - - + -
24H ALA* 3.5 28.0 - - + -
34H PHE* 3.6 22.2 - - + -
118H LEU* 3.0 37.2 + - + +
119H LEU* 3.8 2.0 - - + +
121H VAL* 1.3 76.0 - - - +
123H GLY* 1.3 55.9 + - - +
125H ARG* 4.2 4.3 - - - -
126H LEU* 2.7 39.9 + - + +
130H PHE* 3.6 18.6 - - + -
135H TRP* 3.1 51.1 - - + -
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Residues in contact with GLY 123 (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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36D LEU* 5.8 0.2 - - - +
40D ARG* 3.6 7.3 + - - -
62D TYR* 3.0 23.8 + - - -
119H LEU 2.8 13.4 + - - -
120H HIS 3.4 5.4 - - - -
121H VAL 2.9 0.2 - - - -
122H LEU* 1.3 76.6 - - - +
124H ASP* 1.3 56.4 + - - +
127H GLY* 2.8 32.4 + - - +
130H PHE* 3.8 11.4 - - - -
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Residues in contact with ASP 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ARG* 2.4 39.3 + - - +
37H GLU* 4.2 15.3 - - - +
120H HIS* 3.3 17.3 + - - +
121H VAL* 2.8 14.8 + - - +
123H GLY* 1.3 72.8 - - - +
125H ARG* 1.3 67.7 + - + +
127H GLY* 3.4 7.3 + - - -
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Residues in contact with ARG 125 (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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23H SER 5.7 0.2 - - - -
24H ALA* 4.0 37.1 + - + +
30H GLU 4.3 6.7 + - - -
33H ALA* 4.2 7.5 - - - +
34H PHE* 3.7 45.5 - - + +
37H GLU* 3.3 31.7 + - - -
121H VAL* 3.0 13.3 + - - +
122H LEU* 3.7 6.3 - - - +
124H ASP* 1.3 85.0 - - - +
126H LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G ASP* 5.6 4.0 - - - +
20H GLN* 3.2 62.4 - - + +
23H SER* 4.2 10.5 - - - -
24H ALA* 3.9 23.8 - - + +
122H LEU* 2.7 23.0 + - + +
125H ARG* 1.3 75.7 - - - +
127H GLY* 1.3 60.2 + - - +
128H THR 3.9 1.0 + - - -
129H HIS* 4.0 21.2 + - + +
130H PHE* 3.5 28.9 - - + +
135H TRP* 4.5 2.0 - - + +
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Residues in contact with GLY 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 4.5 4.7 - - - -
62D TYR* 3.1 26.0 - - - -
123H GLY 2.8 21.1 + - - +
124H ASP 3.4 6.9 + - - -
126H LEU* 1.3 74.2 - - - +
128H THR* 1.3 64.1 + - - -
129H HIS* 5.6 0.2 - - - -
130H PHE* 3.4 4.3 - - - +
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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