Contacts of the strand formed by residues 90 - 100 (chain K) in PDB entry 3IT8
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 SER 90 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8K THR* 4.3 9.9 - - - +
9K VAL 3.2 15.7 - - - -
10K THR* 3.5 19.5 - - - +
77K LEU* 4.1 7.6 - - - +
88K THR* 3.1 22.6 - - - +
89K THR* 1.3 80.9 - - - +
91K LEU* 1.3 61.8 + - - +
92K SER* 5.1 1.2 + - - -
112K THR* 3.8 3.7 + - - -
113K ALA* 3.5 21.4 + - - +
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Residues in contact with LEU 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K THR* 3.3 4.7 - - - +
9K VAL* 3.0 40.7 + - + -
73K MET* 3.4 19.6 - - + +
76K THR* 3.6 37.0 - - + -
77K LEU* 4.1 11.9 - - + +
80K ILE* 4.1 13.9 - - + -
90K SER* 1.3 75.7 - - - +
92K SER* 1.3 63.7 + - - +
110K VAL* 3.6 19.3 - - + -
111K GLU 3.5 16.2 - - - +
112K THR* 3.6 16.6 - - - +
117K LEU* 4.5 0.9 - - + -
140K MET* 4.0 12.6 - - + -
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Residues in contact with SER 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ASN* 4.1 7.0 + - - -
7K TYR 3.1 7.2 - - - -
8K THR* 2.9 27.6 + - - +
73K MET* 3.8 4.5 - - - -
90K SER* 5.1 2.1 + - - -
91K LEU* 1.3 73.1 - - - +
93K LEU* 1.3 60.2 + - - +
94K ILE* 3.9 5.8 + - - -
109K TYR 3.9 0.2 - - - +
110K VAL* 3.2 9.1 - - - +
111K GLU* 2.9 56.3 + - - +
325K NAG 4.5 7.0 + - - -
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Residues in contact with LEU 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K TYR 3.4 6.6 - - - +
6K ASN* 3.6 0.5 - - - -
7K TYR* 2.8 55.4 + - + -
69K TRP* 3.7 48.5 - - + -
73K MET* 3.7 10.5 - - + +
92K SER* 1.3 72.3 - - - +
94K ILE* 1.3 63.9 + - - +
95K THR* 5.0 3.1 - - + -
109K TYR 3.6 14.4 - - - +
110K VAL* 3.9 17.5 - - + -
140K MET* 5.0 3.6 - - + -
155K LEU* 4.3 29.6 - - + -
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Residues in contact with ILE 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K LYS* 4.7 4.3 - - + -
5K TYR 3.6 3.6 - - - +
6K ASN* 3.4 37.0 - - + +
92K SER* 4.2 6.3 - - - -
93K LEU* 1.3 74.3 - - - +
95K THR* 1.3 63.6 + - - +
107K TYR* 3.8 6.9 - - + -
108K GLY* 3.2 1.6 + - - -
109K TYR* 2.8 70.4 + - + +
111K GLU* 4.0 16.6 - - + -
248K PRO* 3.4 32.5 - - + -
325K NAG 3.6 18.4 - - + +
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Residues in contact with THR 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K LYS 3.7 0.2 - - - -
5K TYR* 2.7 54.3 + - + +
7K TYR* 4.7 10.5 - - + -
93K LEU* 5.0 5.6 - - + +
94K ILE* 1.3 77.3 - - - +
96K GLY* 1.3 53.0 + - - +
107K TYR* 2.8 26.2 + - - -
108K GLY* 3.9 4.5 - - - -
155K LEU* 3.7 22.8 - - + +
158K PHE* 3.8 24.0 - - + -
159K GLU* 4.7 4.0 - - - +
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Residues in contact with GLY 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K LEU* 3.1 13.9 - - - -
4K LYS* 4.4 0.2 - - - -
5K TYR 4.6 0.2 - - - -
95K THR* 1.3 78.0 + - - +
97K CYS* 1.3 60.2 + - - +
106K SER* 3.3 4.0 - - - -
107K TYR* 2.8 43.6 + - - +
158K PHE* 4.4 3.6 - - - -
159K GLU* 5.8 0.2 - - - -
163K CYS* 3.6 14.5 - - - +
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Residues in contact with CYS 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K THR* 3.9 1.7 + - - +
3K LEU* 2.9 30.4 + - - +
96K GLY* 1.3 75.9 - - - +
98K TYR* 1.3 68.8 + - - +
105K GLY 3.2 15.3 - - - +
106K SER* 3.9 9.6 - - - +
107K TYR* 3.8 6.4 + - - -
163K CYS* 3.1 42.1 - - + -
164K SER* 3.8 11.0 - - - +
167K ILE* 3.8 23.6 - - - -
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Residues in contact with TYR 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K ILE 3.5 11.0 - - - +
2K THR* 3.9 9.9 - - - +
97K CYS* 1.3 83.2 - - - +
99K GLU* 1.3 62.3 + - - +
100K THR* 3.6 22.9 - - - +
103K LEU* 4.1 4.7 - - + +
104K PHE* 3.2 34.1 + - - +
105K GLY* 2.9 48.5 + - - +
106K SER 4.1 2.0 - - - -
107K TYR* 4.5 6.5 - + + -
167K ILE* 4.5 4.5 - - - -
211K ASP* 5.7 0.2 - - + -
213K ILE* 4.3 15.8 - - + +
245K PRO 4.1 10.0 + - - -
246K GLY* 3.7 35.4 - - - +
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Residues in contact with GLU 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H ARG* 3.0 48.2 + - - +
32H ARG* 3.2 29.6 + - - -
1K ILE* 2.9 52.9 + - + +
98K TYR* 1.3 75.0 - - - +
100K THR* 1.3 59.6 + - - +
101K GLY 3.5 3.6 + - - +
103K LEU 3.6 4.9 - - - -
104K PHE* 4.1 10.3 - - + -
164K SER 5.4 1.0 - - - +
167K ILE* 5.0 7.2 - - + +
168K LEU* 4.0 8.6 - - - +
171K GLN* 5.7 0.3 - - - +
286K ASP* 3.0 7.8 - - - +
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Residues in contact with THR 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K TYR* 3.6 22.3 - - - +
99K GLU* 1.3 68.8 - - - +
101K GLY* 1.3 66.0 + - - +
102K LEU 3.2 0.5 + - - -
103K LEU* 3.0 25.1 + - - +
211K ASP* 3.1 43.0 + - - +
212K VAL 4.1 0.9 - - - +
213K ILE* 3.9 25.8 - - + +
284K PHE* 3.3 28.5 - - - +
285K HIS* 4.3 1.8 - - - -
286K ASP* 4.0 0.9 - - - -
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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