Contacts of the helix formed by residues 108 - 121 (chain A) in PDB entry 1K63
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 ASP 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLY* 4.0 4.3 - - - -
38A ASN* 2.7 31.5 + - - +
107A HIS* 1.3 86.7 - - + +
109A TRP* 1.3 77.6 + - - +
111A SER* 2.6 32.9 + - - -
112A ALA 3.3 2.1 + - - -
132A GLU 2.9 23.1 + - - -
133A ALA* 4.6 1.6 - - - +
134A ILE* 4.0 13.5 - - - +
248A LEU* 5.0 0.2 - - - +
272A HIS* 2.8 26.9 + - - +
2001A BRP 2.9 26.2 + - - -
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Residues in contact with TRP 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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37A GLY* 3.8 8.0 - - - -
38A ASN* 3.9 1.6 - - + -
63A LEU* 5.2 0.7 - - + -
82A TYR* 3.6 22.2 - + - -
108A ASP* 1.3 104.2 + - - +
110A GLY* 1.3 57.1 + - - +
112A ALA* 3.3 23.4 + - + +
113A LEU* 3.0 34.8 + - + +
134A ILE* 3.6 13.5 - - + -
207A TRP* 3.3 61.4 + + + -
210A GLN* 3.5 25.1 - - + -
211A ILE* 3.4 31.9 - - + -
212A PRO* 4.1 3.1 - - + -
220A VAL* 4.0 11.2 - - + -
1001A BR 3.4 25.7 - - + +
2001A BRP 3.9 3.0 + - - -
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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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35A GLN* 3.6 20.1 - - - +
36A HIS 3.4 22.8 + - - -
106A VAL* 3.6 12.2 - - - +
107A HIS 2.7 11.2 + - - -
109A TRP* 1.3 80.2 - - - +
111A SER* 1.3 58.1 + - - +
113A LEU* 4.0 3.1 - - - +
114A GLY* 2.8 25.3 + - - -
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Residues in contact with SER 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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106A VAL* 3.5 26.0 - - - +
107A HIS 3.1 9.1 + - - -
108A ASP 2.6 20.0 + - - -
110A GLY* 1.3 77.2 - - - +
112A ALA* 1.3 59.3 + - - -
115A PHE* 2.7 41.4 + - - -
133A ALA* 3.2 22.3 - - - +
134A ILE 3.0 22.2 + - - -
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Residues in contact with ALA 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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82A TYR* 3.2 9.6 + - + -
108A ASP 3.3 2.9 + - - +
109A TRP* 3.3 39.2 + - + +
111A SER* 1.3 82.1 + - - +
113A LEU* 1.3 63.0 + - - +
116A ASP* 3.1 25.6 + - - +
134A ILE* 4.5 5.8 - - + -
220A VAL* 6.2 0.4 - - + -
227A TYR* 3.3 32.6 - - + +
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Residues in contact with LEU 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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63A LEU* 3.7 39.0 - - + -
82A TYR* 3.4 34.5 - - + +
85A HIS* 4.5 4.9 - - + -
86A ARG* 4.0 31.8 - - + +
89A LEU* 4.1 18.4 - - + -
93A TRP* 4.8 2.6 - - - -
109A TRP 3.0 21.4 + - - +
110A GLY* 4.0 4.7 - - - +
112A ALA* 1.3 77.5 - - - +
114A GLY* 1.3 56.7 + - - +
116A ASP* 3.5 1.7 - - - +
117A TRP* 2.9 30.6 + - - +
120A ARG* 5.1 0.9 + - - -
207A TRP* 4.2 11.2 - - + -
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Residues in contact with GLY 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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93A TRP* 4.3 18.6 - - - -
104A LEU* 3.8 10.7 - - - +
106A VAL* 4.3 11.4 - - - -
110A GLY 2.8 22.3 + - - -
111A SER 3.7 0.2 - - - -
113A LEU* 1.3 74.8 - - - +
115A PHE* 1.3 59.0 + - - +
117A TRP* 3.4 2.3 + - - +
118A ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 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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104A LEU* 6.5 0.2 - - + -
106A VAL* 4.0 10.8 - - + -
111A SER* 2.7 29.1 + - - +
114A GLY* 1.3 70.5 - - - -
116A ASP* 1.3 60.4 + - - +
118A ALA* 3.8 5.0 - - - +
119A ARG* 2.9 29.8 + - - +
128A ILE* 3.8 30.3 - - + -
130A TYR* 3.8 28.3 - + + -
133A ALA* 3.9 18.8 - - + -
134A ILE 4.1 1.1 - - - -
135A ALA* 4.1 7.6 - - - -
227A TYR* 3.7 40.1 - + + +
230A TRP* 3.8 3.0 - - - -
231A LEU* 3.5 27.8 - - + -
260A TRP* 4.1 18.4 - + - -
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Residues in contact with ASP 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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82A TYR* 2.5 33.3 + - - +
86A ARG* 2.8 34.8 + - - -
112A ALA 3.1 8.8 + - - +
113A LEU 3.5 2.7 - - - +
115A PHE* 1.3 78.5 - - - +
117A TRP* 1.3 63.9 + - - +
119A ARG* 3.3 12.8 + - - +
120A ARG* 3.0 41.8 + - - +
223A ILE* 3.4 10.6 - - - +
227A TYR* 3.8 15.0 - - + -
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Residues in contact with TRP 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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90A ASP* 3.2 30.1 + - - +
93A TRP* 3.6 46.3 - + + +
98A LEU* 4.7 9.2 - - + -
102A VAL* 4.6 16.2 - - + -
104A LEU* 4.3 12.6 - - + -
113A LEU 2.9 17.8 + - - +
114A GLY 3.8 2.9 - - - +
116A ASP* 1.3 78.4 - - - +
118A ALA* 1.3 62.3 + - - +
120A ARG* 3.0 10.8 + - - +
121A HIS* 2.7 73.7 + + + +
124A ARG* 3.9 41.3 - - + +
125A VAL* 3.8 22.4 - - + -
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Residues in contact with ALA 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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104A LEU* 4.0 8.5 - - + -
114A GLY 2.9 18.2 + - - +
115A PHE* 3.8 4.5 - - - +
116A ASP 3.3 0.2 - - - -
117A TRP* 1.3 74.8 - - - +
119A ARG* 1.3 68.1 + - - +
121A HIS 4.3 0.4 - - - +
122A ARG* 2.9 29.3 + - - +
125A VAL* 3.8 27.8 - - + -
128A ILE* 4.2 9.2 - - + -
230A TRP* 3.6 21.0 - - + -
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Residues in contact with ARG 119 (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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86A ARG* 5.9 1.4 - - - +
115A PHE 2.9 15.0 + - - +
116A ASP* 3.6 15.9 + - - +
117A TRP 3.3 0.2 - - - -
118A ALA* 1.3 77.4 - - - +
120A ARG* 1.3 88.0 + - - +
122A ARG* 2.9 37.1 + - - +
223A ILE 5.3 0.4 + - - -
226A ASP* 3.7 52.0 + - - +
227A TYR* 3.9 5.7 - - + +
230A TRP* 3.5 34.7 - - + -
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Residues in contact with ARG 120 (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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86A ARG* 3.5 25.6 - - - +
90A ASP* 2.8 42.6 + - - -
113A LEU 5.1 1.0 + - - -
116A ASP* 3.0 24.6 + - - +
117A TRP* 3.0 25.8 + - - +
118A ALA 3.0 0.8 - - - -
119A ARG* 1.3 104.7 - - - +
121A HIS* 1.3 87.2 + - + +
122A ARG* 3.7 0.9 - - - -
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Residues in contact with HIS 121 (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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90A ASP* 4.9 1.6 - - - -
117A TRP* 2.7 74.1 + + + +
118A ALA 3.3 3.6 - - - -
120A ARG* 1.3 107.2 + - + +
122A ARG* 1.3 64.8 - - - +
123A GLU 3.3 2.7 - - - -
124A ARG* 3.0 47.0 + - - +
125A VAL* 3.7 6.9 - - - +
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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
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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