Contacts of the strand formed by residues 79 - 90 (chain D) in PDB entry 1KD1
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 MET 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D VAL* 6.2 0.2 - - + -
40D GLY 4.3 3.1 - - - +
41D PHE* 3.0 54.1 - - + -
42D ALA* 3.4 31.9 - - - +
77D PRO 4.1 1.6 - - - +
78D PRO* 1.3 77.1 - - - +
80D ARG* 1.3 72.5 + - - +
144D THR* 3.4 18.4 - - + +
145D HIS 3.5 9.2 - - - +
146D THR* 3.8 20.2 - - + +
147D VAL* 5.1 0.7 - - - -
162D MET* 5.1 3.4 - - + +
164D THR* 5.7 2.5 - - - +
187D GLU* 3.4 1.6 - - - +
188D HIS* 2.9 46.9 + - + +
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PRO* 5.4 1.3 - - + +
79D MET* 1.3 86.4 - - - +
81D ALA* 1.3 60.1 + - - +
82D VAL* 2.9 19.7 + - + +
104D GLU 5.5 3.9 + - - -
105D PHE 4.6 2.2 - - - -
106D HIS* 3.8 41.9 - - - +
144D THR* 3.7 2.6 - - - -
145D HIS* 3.3 45.3 + - + -
147D VAL* 4.6 14.1 - - + +
185D GLY 4.0 15.9 - - - +
186D GLY 3.5 2.9 - - - -
187D GLU* 4.0 31.5 + - + +
188D HIS* 3.8 1.8 - - - -
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ARG* 1.3 67.5 - - - +
82D VAL* 1.3 62.7 + - - +
83D ALA 3.3 2.1 + - - -
142D LEU* 3.7 36.8 - - + -
143D ILE 3.4 8.1 - - - -
144D THR* 4.1 6.7 - - - +
181D ILE* 4.2 6.7 - - + -
182D VAL* 3.8 14.2 - - + +
185D GLY 4.3 0.3 - - - +
186D GLY* 2.9 37.0 + - - +
188D HIS* 3.5 8.0 - - + -
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ARG* 2.9 20.9 + - + +
81D ALA* 1.3 71.7 - - - +
83D ALA* 1.3 62.3 + - - +
101D TRP* 3.3 43.7 - - + -
102D THR* 3.6 13.0 + - - +
104D GLU 5.4 2.5 - - - +
105D PHE* 3.4 26.9 - - + -
109D LEU* 4.4 5.4 - - + -
143D ILE* 3.1 9.3 + - + +
144D THR* 5.7 0.2 - - - -
145D HIS* 3.4 28.3 - - + +
182D VAL* 4.3 3.8 - - - -
185D GLY 5.3 3.6 - - - +
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ALA 3.3 3.6 + - - -
82D VAL* 1.3 83.9 - - - +
84D LEU* 1.3 61.9 + - - +
85D ARG 3.9 0.2 - - - -
99D GLU* 5.0 0.7 - - + -
100D VAL 3.0 15.5 - - - +
101D TRP* 3.4 35.2 - - + +
142D LEU* 3.1 8.8 - - - +
143D ILE* 2.7 40.6 + - + -
182D VAL* 3.8 7.6 - - - -
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ALA* 1.3 70.9 - - - +
85D ARG* 1.3 70.6 + - - +
86D ALA* 4.7 1.8 - - + -
99D GLU* 3.3 4.5 - - - -
100D VAL* 2.9 47.7 + - + +
128D ILE* 3.7 27.5 - - + +
140D LEU* 4.3 18.2 - - + -
141D ARG 3.6 12.1 - - - +
142D LEU* 3.7 12.8 - - + -
166D VAL* 5.5 0.2 - - + -
175D LEU* 5.2 4.7 - - + +
178D ALA* 3.6 28.7 - - + -
179D LEU* 4.4 14.4 - - + -
182D VAL* 3.9 9.4 - - + +
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Residues in contact with ARG 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2670A G 3.3 8.1 - - - +
2671A U 2.8 32.8 + - - +
2672A C 3.6 7.7 + - - -
2819A C 2.6 31.3 + - - -
83D ALA 3.9 2.2 + - - -
84D LEU* 1.3 77.1 - - - +
86D ALA* 1.3 65.3 + - - +
87D TYR* 3.4 28.1 + - + -
96D PRO* 4.0 17.2 - - + +
98D THR 3.6 5.8 - - - +
99D GLU* 2.6 33.1 + - + -
140D LEU* 4.0 1.4 - - - -
141D ARG 2.7 40.6 + - - +
143D ILE* 4.3 13.9 - - + +
163D GLU* 2.8 28.4 + - - +
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 4.0 0.4 + - + -
85D ARG* 1.3 74.4 - - - +
87D TYR* 1.3 56.2 + - - +
96D PRO* 3.5 1.6 - - - +
97D LEU* 2.5 43.9 + - + +
98D THR 3.0 9.4 + - - +
128D ILE* 3.3 37.5 - - + -
137D LEU* 4.1 16.4 - - + -
140D LEU* 4.2 10.3 - - + -
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Residues in contact with TYR 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2672A C 2.7 33.3 + - - -
2673A U 3.9 10.1 - - - -
85D ARG* 3.4 24.4 - - + -
86D ALA* 1.3 77.0 - - - +
88D GLU* 1.3 55.2 + - - +
94D GLN* 4.1 16.4 - - + -
95D ARG 3.4 12.8 - - - -
96D PRO* 3.6 24.2 - - + -
97D LEU* 4.6 0.9 - - - -
137D LEU* 3.4 7.9 - - - +
138D GLY* 2.4 34.2 + - - +
139D ASP* 3.5 34.4 + - - +
141D ARG* 3.7 18.6 - - + -
163D GLU* 2.3 39.8 + - - -
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Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ALA 4.3 0.2 + - - -
87D TYR* 1.3 75.5 - - - +
89D ASP* 1.3 68.4 + - - +
90D THR* 3.4 25.1 + - + +
94D GLN* 3.6 3.1 - - - -
95D ARG* 2.9 37.4 + - + +
96D PRO 5.5 1.7 - - - +
97D LEU* 4.0 29.0 - - + +
131D ALA* 5.7 0.4 - - + -
136D ASP* 3.0 20.9 - - + +
138D GLY* 4.6 0.2 - - - -
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Residues in contact with ASP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D GLU* 1.3 77.9 - - - +
90D THR* 1.3 62.9 + - - +
93D GLY 4.1 3.1 - - - -
94D GLN* 3.7 18.4 + - - +
135D GLY 5.1 2.3 - - - +
136D ASP* 2.7 29.1 + - - +
137D LEU 3.8 14.7 - - - +
138D GLY* 3.7 16.2 - - - -
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Residues in contact with THR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D GLU* 3.4 37.0 - - + +
89D ASP* 1.3 80.9 - - - +
91D PRO* 1.3 64.7 - - - +
92D TYR* 2.8 23.3 + - - +
93D GLY* 2.9 24.3 + - - +
95D ARG* 4.2 18.9 + - + -
144K THR* 2.7 23.3 + - - -
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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