Contacts of the strand formed by residues 141 - 152 (chain C) in PDB entry 3KDH
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 VAL 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C HIS* 4.5 6.2 + - - +
45C ALA* 4.3 6.5 + - - -
46C PRO* 3.9 40.2 - - + -
132C GLU* 4.4 18.2 - - - +
133C PHE 3.3 9.6 - - - +
134C LEU* 4.1 17.7 - - + -
139C GLY 4.4 3.8 - - - +
140C LYS* 1.3 82.9 - - - +
142C TYR* 1.3 65.8 + - - +
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Residues in contact with TYR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 2.6 38.4 + - - +
42C ARG* 3.4 29.2 - - + -
43C ILE 3.5 11.9 - - - +
44C HIS* 3.7 24.0 - + + +
45C ALA 3.6 6.1 - - - +
132C GLU* 3.4 7.7 - - - +
133C PHE* 2.8 72.8 + + + +
134C LEU 5.6 0.4 - - - -
135C ASN* 5.3 13.7 - - + -
140C LYS* 5.3 3.1 - - + -
141C VAL* 1.3 78.1 - - - +
143C THR* 1.3 64.6 + - - +
144C VAL* 4.0 2.9 - - + -
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Residues in contact with THR 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLN 3.7 0.2 - - - +
42C ARG* 3.3 6.2 - - - +
43C ILE* 2.8 39.5 + - - -
45C ALA 2.8 21.1 + - - -
46C PRO 3.4 0.9 + - - -
47C ALA* 3.2 21.1 + - - +
50C VAL* 3.9 10.3 - - + +
130C VAL* 3.4 31.2 - - + -
131C ASN 3.3 9.4 + - - +
132C GLU* 4.6 0.2 - - - -
142C TYR* 1.3 76.7 + - - +
144C VAL* 1.3 73.3 + - - +
145C VAL* 3.9 11.2 - - + -
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 3.8 26.7 - - + -
14C GLU* 4.4 5.6 - - - +
18C LEU* 3.8 21.5 - - + -
41C GLN 3.5 8.1 - - - +
42C ARG* 4.5 5.4 - - + -
129C SER 3.8 1.7 - - - +
131C ASN* 2.8 35.2 + - - +
133C PHE* 3.4 32.3 - - + -
142C TYR* 4.0 12.8 - - + -
143C THR* 1.3 80.4 - - - +
145C VAL* 1.3 64.0 + - - +
146C LEU* 3.9 16.1 + - + +
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ILE 3.8 0.7 - - - +
40C THR* 3.4 5.2 - - - -
41C GLN* 2.8 38.7 + - + +
43C ILE* 3.8 17.3 - - + -
50C VAL* 3.8 29.2 - - + -
54C ILE* 4.6 0.7 - - + -
128C THR* 3.6 28.5 - - + -
129C SER 3.3 4.5 - - - +
130C VAL* 4.4 5.4 - - + -
143C THR* 3.9 7.4 - - + -
144C VAL* 1.3 74.3 - - - +
146C LEU* 1.3 66.8 + - - +
174C LEU* 3.8 24.6 - - + +
177C LEU* 4.1 5.8 - - + -
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Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 4.3 2.7 - - + -
18C LEU* 4.2 20.4 - - + -
21C VAL* 4.3 9.4 - - + -
22C ILE* 3.7 31.2 - - + -
26C HIS* 3.4 19.2 - - + +
38C LEU* 3.9 12.3 - - + -
39C ILE 3.6 2.2 - - - -
40C THR* 3.7 28.0 - - + -
128C THR* 3.2 4.3 - - - +
129C SER* 2.8 49.4 + - - +
131C ASN* 5.4 0.7 - - - +
144C VAL* 3.9 19.7 - - + +
145C VAL* 1.3 77.9 - - - +
147C GLU* 1.3 61.0 + - - +
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Residues in contact with GLU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER 4.0 0.3 - - - +
38C LEU* 3.6 3.1 - - - +
39C ILE* 2.8 39.4 + - - +
63C TYR* 4.8 10.5 + - - -
64C LYS* 6.0 1.9 - - - -
112C PHE* 5.6 2.6 - - - -
124C TYR* 4.4 3.5 + - - -
126C SER* 4.3 14.2 + - - +
127C VAL 3.3 4.0 - - - +
128C THR* 2.7 28.0 + - + +
145C VAL 4.2 0.2 - - - -
146C LEU* 1.3 74.9 - - - +
148C SER* 1.3 67.7 + - - +
149C TYR* 5.1 1.1 - - + -
170C VAL* 3.6 30.4 - - + +
173C ASN* 5.9 1.9 - - - +
174C LEU* 3.6 33.6 - - + +
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Residues in contact with SER 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PRO* 5.6 0.9 - - - -
25C TYR 4.3 0.2 + - - -
26C HIS* 2.8 45.7 + - - +
27C GLN 5.6 0.2 + - - -
37C SER 3.1 13.5 - - - -
38C LEU* 4.0 10.8 - - - -
126C SER* 3.2 6.1 - - - -
127C VAL* 2.9 39.5 + - - +
147C GLU* 1.3 75.5 - - - +
149C TYR* 1.3 62.3 + - - +
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Residues in contact with TYR 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C CYS* 4.0 12.1 - - - -
36C THR* 3.2 24.3 - - - -
37C SER* 3.0 29.4 + - - +
39C ILE* 4.7 5.8 - - + -
124C TYR* 3.7 24.5 - + + +
125C LYS 3.2 12.1 - - - +
126C SER* 4.1 0.9 - - - +
147C GLU* 5.1 1.8 - - + -
148C SER* 1.3 79.2 - - - +
150C THR* 1.3 78.4 + - - +
151C VAL* 4.0 13.9 - - + -
163C LYS* 3.2 24.4 + - - +
166C VAL* 3.4 32.7 - - + +
167C ASP* 2.7 33.8 + - - -
170C VAL* 4.1 12.1 - - + -
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Residues in contact with THR 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLN 5.9 1.6 - - - +
28C PHE* 5.3 7.0 - - + -
29C GLU 6.0 0.4 - - - +
34C THR* 5.3 6.5 - - - -
35C CYS 3.4 6.3 - - - -
36C THR* 3.5 20.4 - - + -
123C ASN 3.5 1.4 + - - +
124C TYR* 3.3 2.8 - - - -
125C LYS* 2.9 57.6 + - + +
149C TYR* 1.3 81.0 - - - +
151C VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C THR* 3.2 5.2 - - - -
35C CYS* 2.9 56.2 + - - -
121C LEU* 3.9 25.1 - - + -
122C LYS 3.5 13.0 - - - +
123C ASN 4.1 2.9 - - - -
124C TYR* 3.9 24.2 - - + -
149C TYR* 4.0 12.6 - - + -
150C THR* 1.3 76.2 - - - +
152C ASP* 1.3 76.4 + - - +
162C THR* 4.2 8.7 - - + -
166C VAL* 4.3 7.6 - - + -
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Residues in contact with ASP 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C THR* 3.5 13.1 + - - +
34C THR* 3.5 17.9 - - - +
121C LEU* 4.2 3.6 - - - +
122C LYS* 3.0 37.2 + - + +
123C ASN* 2.9 32.0 + - - +
151C VAL* 1.3 85.5 - - - +
153C ILE* 1.3 66.3 + - - +
154C PRO* 3.3 9.4 - - - +
162C THR* 4.5 0.2 - - - +
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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