Contacts of the strand formed by residues 184 - 201 (chain D) in PDB entry 1XV2
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 GLY 184 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA* 3.2 19.7 - - - +
62D PHE* 3.6 7.2 - - - -
123D VAL* 3.9 14.5 - - - +
125D MSE 4.0 8.3 - - - +
176D PHE* 3.1 22.7 - - - -
183D TYR* 1.3 87.6 - - - +
185D GLY* 1.3 58.3 + - - -
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Residues in contact with GLY 185 (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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45D GLU* 3.6 27.6 - - - -
47D ILE* 4.4 3.2 - - - +
56D ALA* 4.3 0.9 - - - +
123D VAL* 2.9 13.8 - - - +
124D ARG 3.8 1.1 - - - -
125D MSE 5.0 0.2 - - - -
175D HIS* 3.1 7.3 - - - +
176D PHE* 2.8 32.7 + - - +
184D GLY* 1.3 73.3 - - - -
186D HIS* 1.3 58.1 + - - -
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Residues in contact with HIS 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLU* 3.3 19.0 - - - +
123D VAL* 2.8 19.4 - - - +
124D ARG* 2.9 49.4 + - + +
173D HIS* 3.4 18.8 + + - -
174D ILE 4.6 3.1 - - - -
175D HIS* 3.4 10.9 + - - -
185D GLY* 1.3 70.6 - - - -
187D VAL* 1.3 70.4 + - - +
188D LEU* 3.6 3.5 + - + -
234D GLU* 2.9 53.2 + - + +
804D ZN 2.3 32.4 - - - -
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Residues in contact with VAL 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLN* 4.2 3.2 - - - +
121D MSE 3.9 19.5 - - + -
122D HIS 3.5 6.3 - - - +
123D VAL* 4.3 2.5 - - - +
155D ILE* 5.0 4.5 - - + -
174D ILE* 2.8 62.0 + - + +
175D HIS* 4.2 4.3 - - - +
176D PHE* 4.9 2.2 - - + -
185D GLY 3.5 2.6 + - - -
186D HIS* 1.3 84.4 + - - +
188D LEU* 1.3 63.7 + - - +
189D ASP 3.5 24.9 - - - +
190D PHE* 3.8 18.4 - - + -
234D GLU* 4.3 6.4 - - - +
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Residues in contact with LEU 188 (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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92D GLN* 3.4 16.2 + - - -
122D HIS* 2.8 31.9 + - + +
124D ARG* 3.7 19.3 - - + +
143D GLN* 3.7 15.0 - - - +
145D GLU* 3.6 32.3 - - + +
186D HIS* 3.9 10.8 - - + +
187D VAL* 1.3 74.3 - - - +
189D ASP* 1.3 64.5 + - - +
233D ALA 5.0 0.2 - - - +
234D GLU* 3.9 31.6 - - + -
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Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D SER* 5.9 0.2 - - - -
92D GLN* 3.4 27.3 + - - +
122D HIS* 2.9 46.7 + - + +
187D VAL* 3.5 3.8 - - - +
188D LEU* 1.3 81.9 - - - +
190D PHE* 1.3 84.9 + - - +
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Residues in contact with PHE 190 (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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91D SER* 3.9 0.5 - - - -
92D GLN* 2.9 61.6 + - + +
95D VAL* 3.9 28.9 - - + -
96D PHE* 4.0 15.5 - + - -
114D ILE* 4.3 5.2 - - + -
118D PHE* 3.9 5.2 - + + -
120D HIS* 3.2 21.1 - - - +
121D MSE 4.1 12.3 - - - -
155D ILE* 3.8 26.7 - - + -
174D ILE* 5.1 3.1 - - + -
187D VAL* 3.8 11.7 - - + -
189D ASP* 1.3 86.0 + - - +
191D GLU* 1.3 64.8 + - - +
192D VAL* 3.6 29.2 - - + -
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Residues in contact with GLU 191 (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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89D GLN* 5.0 4.7 - - - +
90D LEU 3.3 24.2 - - - +
91D SER* 4.0 7.4 - - - -
118D PHE* 3.5 4.3 - - - -
119D LYS* 2.7 62.7 + - + +
120D HIS* 3.1 39.4 + - + +
190D PHE* 1.3 78.0 - - - +
192D VAL* 1.3 58.5 + - - +
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Residues in contact with VAL 192 (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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87D LEU* 4.4 2.5 - - + +
88D GLN* 4.2 7.2 - - - +
89D GLN* 3.1 24.2 + - - +
90D LEU* 2.9 29.2 + - + +
95D VAL* 3.9 15.0 - - + -
114D ILE* 4.3 3.6 - - + -
117D THR 4.0 3.4 - - - -
118D PHE* 3.9 14.8 - - + -
119D LYS* 4.1 5.4 - - - +
190D PHE* 3.6 26.7 - - + -
191D GLU* 1.3 74.8 - - - +
193D ASP* 1.3 58.8 + - - +
195D VAL* 3.8 32.8 - - + -
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Residues in contact with ASP 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLN* 3.1 10.9 - - - +
89D GLN* 2.9 28.3 + - - +
117D THR* 2.8 33.4 + - - +
118D PHE 4.2 0.6 - - - +
119D LYS* 3.8 34.8 - - + +
150D ASP* 4.5 9.0 - - - +
191D GLU 3.8 1.2 + - - -
192D VAL* 1.3 71.9 - - - +
194D ASP* 1.3 70.8 + - - +
195D VAL 4.2 0.2 - - - -
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Residues in contact with ASP 194 (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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87D LEU 3.8 1.9 - - - +
88D GLN* 3.8 24.3 + - - +
89D GLN* 5.4 2.9 + - - -
116D GLY* 3.5 3.3 - - - -
117D THR* 3.0 29.6 + - - +
193D ASP* 1.3 95.1 - - - +
195D VAL* 1.3 61.3 + - - +
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Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PRO* 3.3 7.1 - - - +
87D LEU* 3.0 51.6 + - + +
114D ILE* 3.7 25.4 - - + -
115D TYR 3.3 11.2 - - - +
116D GLY* 3.9 11.4 - - - -
117D THR 3.4 17.5 - - - +
118D PHE* 4.2 5.8 - - + -
192D VAL* 3.8 26.9 - - + -
194D ASP* 1.3 81.1 + - - +
196D VAL* 1.3 65.5 + - - +
197D VAL* 4.3 4.9 - - + -
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Residues in contact with VAL 196 (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 THR* 3.6 28.0 - - + -
85D PHE 3.8 7.4 - - - +
86D PRO* 4.9 7.9 - - + -
113D LYS 3.6 1.6 - - - +
114D ILE* 3.6 2.4 - - - -
115D TYR* 3.0 40.2 + - + +
195D VAL* 1.3 77.5 - - - +
197D VAL* 1.3 65.1 + - - +
198D GLU* 4.7 8.6 - - + +
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Residues in contact with VAL 197 (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 LYS 3.9 0.3 - - - +
84D THR* 3.2 7.1 - - - +
85D PHE* 2.7 68.3 + - + +
87D LEU* 3.7 30.7 - - + -
99D ILE* 4.2 18.4 - - + -
112D VAL* 5.3 1.3 - - + -
113D LYS 3.4 6.5 - - - +
114D ILE* 4.2 23.3 - - + -
195D VAL* 4.3 4.0 - - + -
196D VAL* 1.3 76.6 - - - +
198D GLU* 1.3 65.9 + - - +
199D ILE* 4.2 9.0 - - + -
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Residues in contact with GLU 198 (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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79D PHE* 3.7 17.5 - - + -
81D ALA* 3.7 21.0 - - + +
83D LYS 3.4 3.8 - - - -
84D THR* 3.9 21.4 + - + +
112D VAL* 3.4 6.9 - - - +
113D LYS* 3.0 59.3 + - - +
115D TYR* 5.9 1.4 - - - +
196D VAL* 4.7 7.9 - - + +
197D VAL* 1.3 79.1 - - - +
199D ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 199 (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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79D PHE* 4.5 0.7 - - - -
81D ALA* 3.5 2.6 - - - -
82D SER* 2.8 31.9 + - - -
83D LYS* 2.9 17.5 + - + +
85D PHE* 3.7 29.2 - - + -
99D ILE* 3.7 27.1 - - + +
102D GLU* 3.8 17.3 - - + +
103D MSE 3.9 9.2 - - + +
110D SER* 4.3 8.5 - - - -
111D ALA 3.4 8.1 - - - +
112D VAL* 4.3 9.9 - - + -
197D VAL* 4.2 5.6 - - + -
198D GLU* 1.3 80.9 - - - +
200D GLN* 1.3 65.7 + - - +
201D ASN* 3.8 22.2 - - - +
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Residues in contact with GLN 200 (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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3D ASN* 3.7 23.6 + - - +
4D VAL 5.3 0.3 + - - -
77D THR* 3.3 21.4 + - - +
78D ASN 3.2 17.0 - - - +
79D PHE* 3.3 32.6 - - + +
80D LYS* 3.3 31.4 + - - +
82D SER* 4.2 2.0 - - - -
110D SER* 3.1 5.4 - - - -
111D ALA* 2.8 32.9 + - + +
199D ILE* 1.3 74.5 - - - +
201D ASN* 1.3 64.4 + - - +
202D PHE* 3.4 24.5 + - + -
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Residues in contact with ASN 201 (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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3D ASN* 3.2 26.7 + - - +
82D SER* 3.4 25.1 + - - -
83D LYS* 5.8 3.2 - - - +
102D GLU 5.5 1.0 + - - -
103D MSE 3.8 10.5 - - - +
104D LEU* 3.0 54.7 + - + +
105D SER 4.8 0.5 + - - -
108D LEU* 5.0 4.3 - - + -
109D PHE 4.0 4.3 - - - +
110D SER* 4.1 4.0 - - - -
199D ILE* 3.8 10.7 - - - +
200D GLN* 1.3 73.8 - - - +
202D PHE* 1.3 63.1 + - - +
203D GLU 4.0 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