Contacts of the strand formed by residues 212 - 220 (chain P) in PDB entry 1SVC
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 212 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P ASN* 3.8 27.6 + - + +
110P HIS* 3.3 9.7 + - - -
209P ASP* 3.3 39.2 + - + +
210P LEU 3.5 0.4 - - - -
211P SER* 1.3 81.8 - - - +
213P VAL* 1.3 66.5 + - - +
239P ALA* 3.4 32.8 - - + -
240P ILE 3.3 9.6 - - - +
241P TYR* 3.6 24.7 - - + -
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Residues in contact with VAL 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P PHE* 4.0 6.3 - - + -
100P LEU* 3.6 28.9 - - + -
101P VAL 3.7 8.1 - - - +
103P ASN* 5.1 1.6 - - - -
110P HIS* 3.7 21.5 - - + +
112P HIS* 3.9 22.0 - - + -
142P ILE* 3.7 22.4 - - + -
212P VAL* 1.3 81.2 - - - +
214P ARG* 1.3 63.0 + - - +
239P ALA* 3.3 5.9 - - - -
240P ILE* 2.7 45.7 + - + +
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Residues in contact with ARG 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P GLN 3.5 1.9 - - - +
100P LEU* 3.6 7.5 - - - +
101P VAL* 3.0 42.4 + - + -
102P THR 3.5 19.4 + - - +
103P ASN* 3.5 30.1 + - + +
104P GLY 5.2 5.7 + - - -
107P ILE* 5.7 6.2 - - - +
213P VAL* 1.3 79.5 - - - +
215P LEU* 1.3 64.0 + - - +
236P VAL* 3.4 28.7 - - + +
237P SER 3.0 23.6 + - - +
238P ASP* 4.0 12.5 + - - +
239P ALA* 4.1 7.2 - - - +
240P ILE* 5.1 0.4 - - - -
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Residues in contact with LEU 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P PRO* 3.5 36.8 - - + -
70P LEU* 4.5 8.1 - - + -
83P PRO* 5.0 5.6 - - + -
98P VAL* 3.7 18.2 - - + -
99P GLN 3.7 1.8 - - - -
100P LEU* 4.2 18.2 - - + -
114P LEU* 4.3 12.1 - - + -
140P LEU* 4.7 5.4 - - + -
214P ARG* 1.3 74.5 - - - +
216P MET* 1.3 59.7 + - - +
217P PHE* 3.8 28.6 - - + -
235P VAL 3.6 0.9 - - - +
236P VAL* 3.3 3.4 - - - -
237P SER* 2.7 42.3 + - - +
240P ILE* 3.7 18.2 - - + -
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Residues in contact with MET 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97P ILE 3.3 1.9 - - - +
98P VAL* 3.3 4.7 - - - -
99P GLN* 3.0 47.4 + - + +
101P VAL* 3.7 31.4 - - + -
107P ILE* 4.4 17.9 - - + -
167P ASN* 5.0 4.0 - - - +
170P LEU* 4.4 24.7 - - + -
171P LEU* 4.1 13.2 - - + -
215P LEU* 1.3 73.6 - - - +
217P PHE* 1.3 60.6 + - - +
218P THR* 4.0 4.2 + - - +
234P PRO* 3.6 35.2 - - + +
235P VAL 3.2 13.0 - - - +
236P VAL* 4.5 7.6 - - + -
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Residues in contact with PHE 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P LEU* 4.1 23.5 - - + +
47P ILE* 4.4 21.3 - - + -
51P PRO* 5.9 1.3 - - + -
83P PRO* 5.7 5.2 - - + -
85P VAL* 3.6 24.5 - - + -
96P VAL* 5.3 2.7 - - + -
97P ILE 3.0 7.4 - - - +
98P VAL* 3.4 37.5 - - + -
137P PHE* 3.4 29.4 - + - -
140P LEU* 6.0 0.7 - - + -
215P LEU* 3.8 38.4 - - + -
216P MET* 1.3 70.7 - - - +
218P THR* 1.3 62.8 - - - +
234P PRO* 3.1 3.8 - - - +
235P VAL 2.8 44.9 + - - +
237P SER* 4.5 2.0 - - - -
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Residues in contact with THR 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P LEU* 3.9 2.7 - - - -
95P LYS 3.4 2.8 - - - +
96P VAL* 3.2 3.1 - - - -
97P ILE* 2.9 47.3 + - - +
99P GLN* 4.2 4.9 + - - -
167P ASN* 3.5 19.2 + - - +
216P MET* 4.3 3.5 + - - +
217P PHE* 1.3 77.9 + - - +
219P ALA* 1.3 59.2 + - - +
220P PHE* 3.9 6.9 - - + -
231P ARG* 3.6 31.6 - - + -
232P LEU 4.1 1.1 - - - +
234P PRO* 3.5 31.5 - - + +
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Residues in contact with ALA 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P LEU* 3.2 27.2 - - + +
87P ILE* 4.3 13.9 - - + -
94P ALA* 4.8 2.5 - - + -
95P LYS 3.6 3.8 - - - -
96P VAL* 4.0 9.2 - - + -
218P THR* 1.3 72.5 - - - +
220P PHE* 1.3 59.7 + - - +
221P LEU* 3.6 4.2 + - + -
231P ARG* 2.9 23.0 - - - +
232P LEU* 2.9 35.7 + - + +
233P GLU 5.6 0.2 + - - -
234P PRO* 5.5 0.2 - - - +
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Residues in contact with PHE 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P ALA* 3.8 1.5 - - - -
95P LYS* 2.7 60.8 + - + +
97P ILE* 3.7 29.2 - - + -
165P GLY 4.3 11.0 - - - -
166P TYR* 3.7 25.6 - + - -
167P ASN* 4.6 3.4 - - - -
180P GLN* 6.1 1.8 - - + -
181P ALA* 5.1 8.3 - - + -
218P THR* 3.9 15.3 - - + -
219P ALA* 1.3 69.2 - - - +
221P LEU* 1.3 65.6 + - - +
228P PHE* 3.4 18.9 - - + +
229P THR* 3.8 24.5 - - - -
230P ARG 3.6 2.5 - - - -
231P ARG* 3.5 27.8 - - + -
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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