Contacts of the strand formed by residues 95 - 106 (chain D) in PDB entry 5XV1
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 LEU 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D LEU* 3.8 4.4 - - - +
91D GLY 5.1 1.2 + - - -
92D GLY 4.0 11.0 + - - +
93D ASP* 4.8 4.0 - - + +
94D GLY* 1.3 74.5 - - - +
96D GLY* 1.3 64.7 + - - +
97D GLN* 5.9 2.2 - - + +
125D LYS* 5.2 21.8 - - + +
126D VAL 3.7 11.4 - - - +
127D HIS* 4.6 21.1 - - + -
196D ILE* 3.7 9.5 - - - +
197D THR* 3.5 49.2 + - - +
198D ASP 5.2 2.7 - - - +
199D ALA* 5.0 17.9 - - + +
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Residues in contact with GLY 96 (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 PHE* 3.4 18.6 - - - -
87D LEU* 3.7 12.6 - - - +
95D LEU* 1.3 80.2 - - - +
97D GLN* 1.3 60.5 + - - +
125D LYS* 3.5 2.3 - - - +
126D VAL 2.6 41.7 + - - +
195D GLN 3.6 8.3 - - - -
196D ILE* 4.5 0.2 - - - -
197D THR* 5.0 0.4 - - - -
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Residues in contact with GLN 97 (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 PHE* 3.3 4.6 - - - -
95D LEU* 5.9 2.4 - - + +
96D GLY* 1.3 76.1 - - - +
98D MET* 1.3 63.3 + - - +
99D SER* 4.3 6.1 + - - -
123D THR* 3.5 22.2 - - + +
124D VAL 3.2 14.6 - - - +
125D LYS* 3.9 30.5 + - + +
194D PHE* 3.2 4.9 - - - +
195D GLN* 2.9 64.4 + - + +
197D THR* 4.4 12.2 + - - +
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Residues in contact with MET 98 (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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21D MET* 3.4 32.1 - - + -
25D LEU* 4.5 9.2 - - + -
79D VAL* 4.4 4.7 - - + -
80D VAL* 3.6 33.9 - - + -
83D PHE* 3.5 42.1 - - + -
97D GLN* 1.3 73.7 - - - +
99D SER* 1.3 63.7 + - - +
122D TRP 3.7 1.1 - - - +
123D THR* 3.2 4.3 - - - +
124D VAL* 2.9 33.6 + - + +
192D ILE* 3.6 32.1 - - + -
193D SER 3.4 9.2 - - - +
194D PHE* 4.0 4.5 - - + -
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Residues in contact with SER 99 (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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25D LEU* 5.7 0.7 - - - -
97D GLN* 4.3 6.8 + - - -
98D MET* 1.3 73.5 - - - +
100D LEU* 1.3 59.1 + - - +
101D GLU* 4.1 2.5 - - - -
121D VAL* 4.5 9.8 - - - +
122D TRP 3.1 4.5 - - - -
123D THR* 3.0 30.1 + - - +
191D LYS 3.8 0.5 - - - +
192D ILE* 2.9 8.5 - - - +
193D SER* 2.9 45.0 + - - -
194D PHE* 6.0 0.2 - - - -
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Residues in contact with LEU 100 (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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25D LEU* 3.9 28.4 - - + +
28D VAL* 3.5 41.1 - - + -
29D LEU* 4.5 9.4 - - + -
99D SER* 1.3 72.5 - - - +
101D GLU* 1.3 57.9 + - - +
102D PHE* 3.7 26.2 - - + -
121D VAL* 3.3 1.1 - - - -
122D TRP* 2.6 50.7 + - + +
190D TYR* 3.9 19.7 - - + -
191D LYS 3.7 2.0 - - - -
192D ILE* 3.4 26.0 - - + -
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Residues in contact with GLU 101 (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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99D SER* 5.4 2.0 - - - -
100D LEU* 1.3 76.2 - - - +
102D PHE* 1.3 65.8 + - - +
103D TYR* 4.1 12.0 - - - +
116D CYS* 5.6 0.5 - - - +
118D PRO* 2.9 40.3 - - + +
120D GLU 3.3 11.2 - - - +
121D VAL* 4.0 15.7 - - + +
190D TYR* 3.3 3.1 - - - -
191D LYS* 2.8 60.4 + - - +
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Residues in contact with PHE 102 (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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28D VAL* 4.0 2.2 - - + -
29D LEU* 3.9 14.1 - - + -
32D ARG* 3.5 37.5 - - + -
100D LEU* 3.7 28.9 - - + -
101D GLU* 1.3 73.6 - - - +
103D TYR* 1.3 60.8 + - - +
118D PRO* 3.5 4.0 - - - +
119D TRP* 2.9 54.5 + + + -
120D GLU* 2.7 30.0 + - + +
122D TRP* 3.8 19.3 - + - -
188D TYR* 3.8 15.5 - - + -
189D LEU 3.3 7.0 - - - +
190D TYR* 3.5 28.5 - - + -
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Residues in contact with TYR 103 (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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101D GLU* 4.1 16.6 - - - +
102D PHE* 1.3 75.6 - - - +
104D GLN* 1.3 65.5 + - - +
105D LYS* 4.4 10.3 + - + -
116D CYS* 3.5 37.6 - - + -
117D ILE 3.1 22.2 - - - +
118D PRO* 3.9 4.3 - - + -
119D TRP* 3.6 9.3 + - - +
176D ASN 4.3 0.3 - - - +
177D VAL 4.5 2.4 - - - +
189D LEU* 3.1 58.6 + - + +
190D TYR 3.8 14.6 + - - -
191D LYS* 3.7 25.7 - - + +
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Residues in contact with GLN 104 (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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103D TYR* 1.3 77.5 - - - +
105D LYS* 1.3 62.7 + - - +
106D LYS* 6.2 0.2 - - + -
115D GLU 3.5 0.2 - - - +
116D CYS* 3.4 4.5 - - - -
117D ILE* 2.9 47.3 + - + +
119D TRP* 3.4 21.7 - - + +
164D TYR* 2.3 29.8 + - - -
166D PRO* 3.3 26.2 - - + +
167D LYS* 4.8 4.8 - - - +
176D ASN* 3.4 9.2 - - + +
177D VAL* 4.3 13.8 - - + +
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Residues in contact with LYS 105 (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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103D TYR* 4.2 14.3 + - + +
104D GLN* 1.3 76.5 - - - +
106D LYS* 1.3 61.9 + - - +
107D LYS 4.3 0.2 - - - -
114D ASP* 4.9 21.6 + - + +
115D GLU 3.6 2.7 - - - +
116D CYS* 4.2 20.1 - - - -
175D ASP* 3.4 22.4 - - - +
176D ASN* 2.7 47.0 + - - +
189D LEU* 3.8 12.6 - - + -
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Residues in contact with LYS 106 (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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104D GLN* 6.2 0.2 - - + -
105D LYS* 1.3 75.6 - - - +
107D LYS* 1.3 78.2 + - - +
108D SER* 5.1 0.4 + - - -
114D ASP* 3.4 4.9 - - - -
115D GLU* 2.9 68.8 + - + +
117D ILE* 5.0 10.1 - - + -
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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