Contacts of the helix formed by residues 108 - 118 (chain A) in PDB entry 4NFT
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TYR* 4.2 10.3 - - + -
9A TYR* 3.5 48.7 - - + +
100A SER* 3.4 5.2 - - - +
106A GLN 3.7 1.3 - - - +
107A PHE* 1.3 93.4 - - + +
109A VAL* 1.3 66.6 + - - +
110A GLY 3.5 1.6 - - - +
111A ARG* 3.8 26.7 - - + -
112A ILE* 3.1 24.1 + - + +
174C GLU* 5.6 4.0 - - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 3.6 48.9 - - + +
100A SER* 3.1 30.8 + - - +
103A ALA* 5.1 0.4 - - + -
105A LEU* 4.5 6.7 - - + -
107A PHE 3.4 4.0 + - - +
108A PRO* 1.3 71.0 - - - +
110A GLY* 1.3 58.0 + - - +
112A ILE* 3.3 5.7 + - - +
113A HIS* 2.9 28.3 + - - +
131A ALA* 3.9 9.7 - - + +
132A VAL* 3.9 22.7 - - + +
135A ALA* 4.3 15.3 - - + -
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 4.8 9.1 - - - +
108A PRO* 3.5 0.6 - - - +
109A VAL* 1.3 78.1 - - - +
111A ARG* 1.3 62.0 + - - +
113A HIS* 3.2 8.5 + - - +
114A ARG* 3.2 35.1 + - - -
144C GLU* 5.7 0.2 - - - -
172C GLY 6.0 0.2 + - - -
173C ASP* 3.1 26.0 - - - +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLU* 3.7 9.3 + - - +
5A SER* 2.4 35.9 + - - +
6A TYR* 3.5 23.1 + - + +
9A TYR* 3.6 24.7 + - - +
108A PRO* 3.5 26.6 + - + +
109A VAL 3.4 0.8 - - - -
110A GLY* 1.3 74.9 - - - +
112A ILE* 1.3 58.6 + - - +
114A ARG* 3.4 10.1 + - - +
115A HIS* 2.9 28.0 + - - +
74C GLU* 3.5 33.8 + - - +
78C HIS* 4.6 2.0 + - - -
175C GLU* 3.4 39.0 + - + +
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TYR* 3.9 18.6 - - + +
39A PHE* 4.2 10.3 - - + -
107A PHE* 3.9 24.2 - - + -
108A PRO* 3.1 23.6 + - + +
109A VAL 3.8 2.7 - - - +
111A ARG* 1.3 75.2 - - - +
113A HIS* 1.3 60.8 + - - +
115A HIS* 3.2 5.5 + - - +
116A LEU* 2.8 30.9 + - + +
131A ALA* 3.8 22.7 - - - +
134A SER* 4.0 18.4 - - - -
135A ALA* 3.6 27.6 - - + -
138A LEU* 3.9 12.3 - - + -
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Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG* 3.6 21.8 + - - +
109A VAL 2.9 17.0 + - - +
110A GLY* 3.5 7.4 - - - +
112A ILE* 1.3 76.9 - - - +
114A ARG* 1.3 57.5 + - - +
116A LEU* 3.2 7.1 + - - +
117A LYS* 3.0 46.9 + - + +
126A VAL* 3.8 27.8 - - + +
127A GLY 4.1 6.8 + - - -
128A ALA* 5.4 1.1 - - - -
131A ALA* 3.7 18.5 - - + +
144C GLU* 4.0 17.5 - - - +
147C GLU* 3.1 32.3 + - + +
148C LEU* 4.9 8.9 - - + +
151C ASN* 5.3 4.9 - - - -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY* 3.2 25.1 + - - +
111A ARG* 3.8 10.5 - - - +
113A HIS* 1.3 76.6 - - - +
115A HIS* 1.3 66.5 + - - +
117A LYS* 3.4 9.0 + - - +
118A SER* 3.1 23.9 + - - -
75C LEU* 4.2 20.1 - - - +
78C HIS* 3.7 19.3 + - + -
140C TYR* 3.1 28.6 + - - +
144C GLU* 2.8 38.5 + - - +
148C LEU* 4.9 0.4 - - - +
173C ASP* 2.4 41.2 + - - -
175C GLU* 2.6 35.2 + - - +
176C LEU* 4.2 9.4 - - - +
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Residues in contact with HIS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.4 26.9 - - + +
2A ARG 4.4 1.0 + - - -
4A GLU* 3.2 36.3 + - + +
6A TYR* 3.0 23.4 + + - +
36A ASN* 3.7 16.8 - - - -
39A PHE* 3.3 30.4 - + + -
111A ARG 2.9 17.4 + - - +
112A ILE 3.2 5.1 + - - +
114A ARG* 1.3 78.1 - - - +
116A LEU* 1.3 61.6 + - - +
118A SER* 3.0 24.9 + - - -
119A ARG* 3.3 15.3 - - + +
78C HIS* 3.9 7.5 + - - -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 3.7 20.2 - - + -
43A ALA* 4.1 17.3 - - + -
58A ILE* 4.5 18.5 - - + +
63A ILE* 4.6 13.5 - - + -
112A ILE 2.8 15.4 + - - +
113A HIS 3.3 8.5 - - - +
115A HIS* 1.3 76.0 - - - +
117A LYS* 1.3 62.8 + - - +
119A ARG* 3.0 16.9 + - + +
120A THR* 3.3 10.0 + - - -
126A VAL* 3.9 25.5 - - + +
130A ALA* 4.1 6.3 - - + +
131A ALA* 4.0 20.4 - - + -
134A SER* 3.8 21.5 - - - +
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Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A HIS* 3.0 38.6 + - - +
114A ARG* 3.4 12.1 + - - +
116A LEU* 1.3 75.0 - - - +
118A SER* 1.3 59.4 + - - +
120A THR* 3.2 30.3 + - + +
126A VAL* 3.6 24.5 - - + +
140C TYR* 4.9 14.5 - - + -
143C ALA* 5.3 2.6 - - - +
144C GLU* 2.2 39.9 + - - +
147C GLU* 3.5 24.9 + - - +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ARG 3.1 13.5 + - - -
115A HIS* 3.0 17.0 + - - -
116A LEU 3.1 1.0 - - - -
117A LYS* 1.3 78.7 - - - +
119A ARG* 1.3 77.7 + - - +
120A THR 3.3 3.4 - - - +
78C HIS* 3.8 23.3 - - - -
82C GLU* 5.9 1.8 - - - -
85C LYS* 4.2 22.4 + - - +
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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