Contacts of the helix formed by residues 114 - 132 (chain H) in PDB entry 6NZD
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 HIS 114 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLN* 5.6 2.2 - - - -
111H HIS 5.6 1.1 - - - -
113H SER* 1.3 88.1 + - - +
115H PRO* 1.3 72.5 - - + +
116H GLN* 3.3 44.3 - - + +
117H LEU* 3.1 24.8 + - + +
118H PHE* 2.9 26.1 + - - +
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Residues in contact with PRO 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F LEU 5.1 0.4 - - - +
132F VAL* 6.0 4.5 - - + -
133F GLN* 5.4 11.9 - - + +
136F GLN* 4.6 29.2 - - + +
113H SER 4.1 4.0 - - - +
114H HIS* 1.3 103.2 - - + +
116H GLN* 1.3 59.2 + - + +
118H PHE* 3.7 11.4 - - + +
119H SER* 2.9 33.1 + - - -
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Residues in contact with GLN 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ARG* 3.2 38.7 + - - +
114H HIS* 3.3 25.2 - - + +
115H PRO* 1.3 78.7 - - + +
117H LEU* 1.3 64.3 + - + +
119H SER* 4.1 10.0 + - - +
120H ILE* 3.3 34.5 + - + +
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Residues in contact with LEU 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H ASN* 4.5 12.1 - - - +
4H ILE* 4.0 29.8 - - + -
23H GLU* 5.7 6.5 - - - +
112H PRO* 5.9 7.0 - - + -
113H SER* 5.1 6.3 - - - +
114H HIS* 3.1 30.7 + - + +
116H GLN* 1.3 81.6 - - + +
118H PHE* 1.3 60.2 + - - +
120H ILE* 3.4 13.0 + - + +
121H VAL* 3.0 36.0 + - + +
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Residues in contact with PHE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ASP 3.9 10.3 - - - -
131F LEU* 3.4 15.3 - - - -
132F VAL* 3.3 46.9 - - - -
133F GLN* 4.0 20.9 - - - +
137F ARG* 5.3 0.7 - - - -
18H THR* 5.1 0.7 - - + -
111H HIS* 3.4 55.6 - + + +
114H HIS 2.9 12.7 + - - +
115H PRO* 3.3 11.4 + - + +
117H LEU* 1.3 77.4 - - - +
119H SER* 1.3 56.7 + - - +
121H VAL* 3.5 3.1 + - - +
122H ARG* 2.9 45.2 + - + +
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Residues in contact with SER 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F VAL 5.3 2.9 + - - -
95F GLU* 5.4 2.8 + - - -
131F LEU* 3.2 42.1 + - - +
115H PRO 2.9 18.0 + - - -
116H GLN* 4.3 13.3 + - - -
117H LEU 3.3 0.2 - - - -
118H PHE* 1.3 75.8 - - - +
120H ILE* 1.3 59.3 + - - +
123H GLN* 2.9 36.4 + - - +
148H HIS* 5.2 4.0 - - - -
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Residues in contact with ILE 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ILE* 5.6 3.8 - - + -
116H GLN* 3.3 26.6 + - + +
117H LEU* 3.4 13.2 + - + +
118H PHE 3.3 0.6 - - - -
119H SER* 1.3 78.9 - - - +
121H VAL* 1.3 59.7 + - + +
123H GLN* 3.9 1.0 - - - +
124H ALA* 2.9 29.6 + - - +
147H GLN 5.2 3.1 - - - +
148H HIS* 3.4 44.8 - - + +
149H GLY* 5.1 0.7 - - - -
175H ILE* 4.0 21.5 - - + -
177H MET* 5.2 13.0 - - + -
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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
----------------------------------------------------------
4H ILE* 4.2 18.2 - - + -
6H ALA* 4.6 6.5 - - + -
18H THR* 4.0 17.7 - - + +
21H CYS* 3.7 32.8 - - - -
111H HIS* 4.4 10.3 - - + -
117H LEU* 3.0 24.4 + - + +
118H PHE* 4.0 5.4 - - - +
120H ILE* 1.3 75.9 - - + +
122H ARG* 1.3 58.4 + - - +
124H ALA* 3.8 0.9 - - - +
125H CYS* 2.9 29.7 + - + +
173H ILE* 4.7 0.8 - - + +
175H ILE* 3.8 22.2 - - + +
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Residues in contact with ARG 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ASP* 2.8 42.9 + - - +
131F LEU* 3.7 28.5 - - + -
165F TRP* 3.9 19.4 - - - +
500F GDP 3.5 16.1 + - - +
16H PRO* 4.3 18.1 - - - +
17H ARG 5.8 2.5 - - - +
18H THR* 4.5 18.3 - - - +
118H PHE* 2.9 32.1 + - + +
119H SER 3.9 2.7 - - - +
121H VAL* 1.3 77.7 - - - +
123H GLN* 1.3 57.3 + - - +
125H CYS* 3.4 3.9 + - - -
126H VAL* 2.9 53.7 + - - +
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Residues in contact with GLN 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F GLU* 4.7 7.4 + - - -
128F LYS* 5.2 9.9 - - - +
131F LEU* 3.7 20.2 - - + -
500F GDP 4.1 20.3 + - - +
119H SER 2.9 20.8 + - - +
120H ILE 4.0 1.8 - - - +
122H ARG* 1.3 76.0 - - - +
124H ALA* 1.3 57.9 + - - +
126H VAL* 3.3 17.4 - - - +
127H ARG* 3.0 41.7 + - + +
148H HIS* 3.3 43.1 + - + +
149I SER* 5.0 9.1 + - - -
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Residues in contact with ALA 124 (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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120H ILE 2.9 18.6 + - - +
121H VAL 4.0 0.2 - - - +
123H GLN* 1.3 76.3 - - - +
125H CYS* 1.3 59.6 + - - +
127H ARG* 3.5 5.6 + - - +
128H SER* 2.9 28.6 + - - -
143H PHE* 3.9 6.1 - - - -
148H HIS* 5.1 7.1 - - + +
151H VAL* 4.5 14.4 - - + -
173H ILE* 3.6 18.9 - - + +
175H ILE* 3.8 17.5 - - + -
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Residues in contact with CYS 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H CYS* 2.0 50.5 - - - -
16H PRO* 4.5 12.5 - - + +
18H THR* 3.7 24.5 - - + +
121H VAL* 2.9 20.3 + - + +
122H ARG* 3.9 4.5 - - - +
124H ALA* 1.3 74.9 - - - +
126H VAL* 1.3 60.5 + - - +
128H SER* 3.7 2.4 - - - -
129H LEU* 2.9 27.7 + - - +
173H ILE* 3.7 9.1 - - + +
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Residues in contact with VAL 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F TRP* 3.6 41.1 - - + -
500F GDP 3.6 20.6 - - + +
16H PRO* 4.1 14.3 - - + +
122H ARG* 2.9 40.4 + - - +
123H GLN* 3.3 20.6 - - - +
125H CYS* 1.3 76.4 - - - +
127H ARG* 1.3 60.3 + - + +
129H LEU* 5.2 0.2 - - - -
130H SER* 2.8 38.2 + - - +
131H CYS* 4.7 0.2 - - - -
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Residues in contact with ARG 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500F GDP 6.2 0.2 - - - +
123H GLN* 3.0 29.7 + - - +
124H ALA* 4.0 1.3 - - - +
126H VAL* 1.3 83.1 - - + +
128H SER* 1.3 59.3 + - - +
131H CYS* 3.3 42.5 + - - +
132H GLU* 3.5 10.0 + - - +
143H PHE* 3.6 42.1 - - + -
144H GLY* 5.1 8.1 - - - -
145H ASP* 5.2 6.1 - - - +
148I MET* 4.4 22.5 - - - +
149I SER* 5.1 13.2 + - - +
154I THR* 4.6 16.0 - - - +
156I LYS* 4.3 20.2 - - - +
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Residues in contact with SER 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H CYS* 5.8 1.1 - - - -
124H ALA 2.9 17.7 + - - -
125H CYS* 3.2 8.0 + - - -
127H ARG* 1.3 79.6 - - - +
129H LEU* 1.3 61.1 + - - +
130H SER 3.3 1.1 + - - -
132H GLU* 3.7 24.2 - - - +
143H PHE* 3.7 15.0 - - - -
153H SER* 3.6 19.0 - - - -
155H THR* 4.1 12.3 - - - +
169H TRP* 4.8 0.2 - - - -
171H SER* 3.5 22.0 + - - -
173H ILE* 4.5 6.5 - - - -
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Residues in contact with LEU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H CYS* 3.7 24.0 - - + -
9H HIS 4.2 0.7 - - - +
10H PHE* 3.6 49.1 - - + +
16H PRO* 3.9 14.8 - - + +
125H CYS 2.9 14.1 + - - +
126H VAL 3.8 0.7 - - - +
128H SER* 1.3 79.3 - - - +
130H SER* 1.3 58.4 + - - +
132H GLU 5.2 0.2 - - - -
155H THR* 4.3 2.7 - - + -
169H TRP* 3.2 63.8 - - + +
171H SER* 3.9 23.8 - - - -
228H PRO* 5.8 2.6 - - - +
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Residues in contact with SER 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F TRP* 4.2 17.0 - - - -
10H PHE* 6.0 2.2 - - - -
16H PRO* 6.2 1.1 - - - -
126H VAL* 2.8 30.4 + - - -
129H LEU* 1.3 80.6 - - - +
131H CYS* 1.3 60.2 + - - +
132H GLU 4.0 1.3 - - - -
169H TRP* 5.3 0.7 - - - -
228H PRO* 5.7 11.0 - - - +
145I SER* 3.9 8.3 + - - -
146I VAL* 3.3 33.6 - - - +
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Residues in contact with CYS 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500F GDP 5.8 2.5 - - - -
127H ARG* 3.3 43.0 + - - +
130H SER* 1.3 88.0 - - - +
132H GLU* 1.3 73.0 + - - +
133H VAL* 4.1 7.8 + - - +
140I GLU 5.0 0.3 - - - +
141I MET 5.0 2.3 - - - +
144I GLY* 3.4 25.7 + - - -
145I SER* 3.7 9.4 + - - +
146I VAL* 3.7 13.0 - - - -
147I ALA 3.7 22.4 - - - -
148I MET* 5.6 0.2 - - - -
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Residues in contact with GLU 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ARG* 3.5 9.1 + - - +
128H SER* 3.7 19.1 + - - +
130H SER 5.1 0.5 - - - -
131H CYS* 1.3 103.0 + - - +
133H VAL* 1.3 62.2 + - - +
134H CYS* 5.2 2.2 - - - -
137H ARG* 4.1 8.1 + - - -
141H ILE* 3.4 34.8 - - + +
143H PHE* 3.7 38.7 - - + -
153H SER* 4.7 1.8 - - - +
155H THR* 5.3 4.6 - - + +
169H TRP* 4.3 8.5 - - - -
141I MET 4.2 3.7 - - - +
144I GLY* 4.6 0.9 - - - -
156I LYS* 3.8 19.5 - - - +
158I HIS* 3.4 16.1 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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