Contacts of the strand formed by residues 119 - 130 (chain A) in PDB entry 1KIX
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 ILE 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A TYR* 3.8 27.6 - - + -
56A ALA 3.3 13.0 - - - +
57A VAL* 4.2 8.1 - - + -
58A VAL* 4.9 0.9 - - - -
117A GLY 4.5 0.4 - - - +
118A ASP* 1.3 75.1 - - - +
120A ILE* 1.3 64.1 + - - +
147A ALA 3.7 0.2 - - - +
148A LEU* 3.3 8.0 - - - +
149A PHE* 2.7 47.3 + - + +
151A THR* 3.5 12.3 + - - +
189A LEU* 4.2 9.6 - - + -
192A LEU* 3.5 34.3 - - + +
193A ARG* 3.6 33.2 - - + +
196A ALA* 4.9 0.9 - - + -
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Residues in contact with ILE 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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54A PHE* 3.9 2.3 - - + +
55A TYR* 3.4 2.4 - - - -
56A ALA* 2.8 46.0 + - + +
58A VAL* 3.7 18.2 - - + -
76A LEU* 3.9 23.1 - - + -
78A ILE* 4.5 12.1 - - + -
100A LEU* 4.2 13.7 - - + -
102A LEU* 4.4 7.0 - - + -
111A PRO* 4.8 1.1 - - + -
113A ILE* 4.5 2.0 - - + -
118A ASP 4.3 0.4 + - - -
119A ILE* 1.3 79.1 - - - +
121A ARG* 1.3 64.4 + - - +
122A VAL* 4.2 17.4 + - + -
146A TRP* 4.3 13.9 - - + -
147A ALA 3.2 9.4 - - - +
148A LEU* 3.7 17.0 - - + -
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Residues in contact with ARG 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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38A TYR* 4.1 5.6 - - + -
54A PHE 3.4 5.6 - - - +
55A TYR* 3.3 31.2 + - + +
120A ILE* 1.3 74.1 - - - +
122A VAL* 1.3 63.2 + - - +
123A HIS* 3.7 33.3 + - - +
145A SER* 3.8 4.9 + - - +
146A TRP* 3.1 8.9 + - - -
147A ALA* 2.8 53.4 + - + +
149A PHE* 3.9 21.1 - - + -
171A PRO* 5.3 3.0 - - - +
174A PHE* 5.8 1.0 - - - +
176A SER* 5.5 3.2 + - - -
178A HIS* 4.5 14.3 + - - +
180A THR 4.0 15.4 + - - -
181A ILE* 4.3 4.0 - - - +
185A GLU* 2.8 47.6 + - - -
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Residues in contact with VAL 122 (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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53A HIS* 3.3 7.1 - - - +
54A PHE* 2.9 61.4 + - + +
100A LEU* 3.9 20.0 - - + -
102A LEU* 4.7 3.6 - - + -
120A ILE* 4.2 13.5 - - + -
121A ARG* 1.3 77.9 - - - +
123A HIS* 1.3 71.8 + - - +
125A ALA* 3.7 27.6 - - + -
138A ALA* 4.1 15.0 - - + -
145A SER 3.4 9.6 - - - +
146A TRP* 4.6 4.0 - - + -
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Residues in contact with HIS 123 (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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36A TYR* 3.4 48.2 + + + +
38A TYR* 2.8 43.0 + + - -
53A HIS* 3.4 5.8 - - + +
121A ARG* 3.7 32.7 + - - -
122A VAL* 1.3 77.3 - - - +
124A ARG* 1.3 73.8 + - + +
143A SER 5.5 1.1 - - - +
144A SER* 3.2 3.6 - - - -
145A SER* 3.0 46.6 + - - +
185A GLU* 5.0 0.9 - - - -
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Residues in contact with ARG 124 (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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36A TYR* 4.9 7.9 - - + +
51A PRO* 3.7 24.5 - - + +
52A GLN 3.2 4.0 + - - -
53A HIS* 2.7 31.0 + - + -
123A HIS* 1.3 77.6 - - + +
125A ALA* 1.3 56.8 + - - +
138A ALA* 4.0 0.9 - - - +
143A SER* 2.4 46.5 + - - +
144A SER* 2.4 32.9 + - - +
2D T 2.7 42.9 + - - +
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Residues in contact with ALA 125 (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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50A GLN 4.4 0.3 - - - +
51A PRO* 4.0 1.4 - - - +
52A GLN* 2.7 43.1 + - + +
54A PHE* 3.9 18.2 - - + -
100A LEU* 5.2 0.4 - - + -
122A VAL* 3.7 23.3 - - + -
124A ARG* 1.3 75.6 - - - +
126A THR* 1.3 64.0 + - - +
136A PHE* 4.6 4.9 - - + -
137A ASN 3.0 14.6 - - - +
138A ALA* 4.2 0.9 - - + -
2D T 3.8 4.7 - - - +
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Residues in contact with THR 126 (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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47A THR 4.1 3.1 - - - +
48A SER* 3.7 34.7 - - - +
50A GLN 5.4 1.8 - - - +
52A GLN* 5.3 0.7 - - - +
125A ALA* 1.3 75.7 - - - +
127A LEU* 1.3 60.0 + - - +
128A ARG* 5.6 2.5 - - - -
136A PHE* 3.1 8.1 - - - +
137A ASN* 2.7 52.6 + - - +
2D T 3.4 48.0 + - + +
4D T 4.3 4.5 + - - +
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Residues in contact with LEU 127 (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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44A ALA* 3.7 34.8 - - + +
45A SER 3.7 17.5 - - - +
46A LEU* 3.8 17.1 - - + +
47A THR* 3.2 28.6 + - - +
48A SER* 4.2 1.6 + - - -
52A GLN* 4.2 3.3 - - - +
126A THR* 1.3 77.9 - - - +
128A ARG* 1.3 71.6 + - - +
134A ARG* 3.7 30.1 - - + +
135A GLN 3.5 29.4 - - - +
136A PHE* 3.8 21.1 - - + -
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Residues in contact with ARG 128 (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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46A LEU* 3.9 7.9 - - - -
48A SER* 5.8 7.4 - - - -
126A THR* 5.6 3.1 - - - +
127A LEU* 1.3 77.3 - - - +
129A LEU* 1.3 71.7 + - - +
134A ARG* 3.8 0.7 - - - -
135A GLN* 2.8 48.2 + - - +
137A ASN* 3.7 19.7 - - - +
3D T 3.4 21.5 + - - -
4D T 2.9 30.6 - - - +
5D G 4.2 14.1 + - - -
6D G 3.7 18.6 - - - +
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Residues in contact with LEU 129 (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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46A LEU* 4.0 32.3 - - + +
128A ARG* 1.3 85.2 + - - +
130A TYR* 1.3 62.0 + - - +
132A GLY* 5.1 6.1 - - - +
133A GLN 3.4 20.4 - - - +
134A ARG* 4.4 13.2 - - + +
6D G 5.4 0.2 + - - -
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Residues in contact with TYR 130 (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 THR* 5.8 0.7 - - - -
128A ARG 3.8 0.2 + - - -
129A LEU* 1.3 77.2 - - - +
131A ASN* 1.3 106.8 + - + +
132A GLY 3.0 1.1 - - - -
133A GLN* 2.9 25.1 + - - +
135A GLN* 3.2 38.3 - - + +
6D G 3.4 73.0 + + + +
7D G 5.4 2.5 - - - -
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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