Contacts of the strand formed by residues 199 - 204 (chain B) in PDB entry 3DPR
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 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER* 3.2 4.8 + - - -
27B ASP 4.1 0.4 + - - -
28B VAL* 2.7 39.0 - - - +
29B ALA* 4.4 2.6 + - - +
109B HIS* 3.1 20.7 - - - -
110B VAL 3.1 13.2 - - - -
111B GLN* 3.7 7.6 - - - -
192B ILE* 3.4 7.4 - - - +
197B ASN* 3.3 13.7 + - - +
198B ASN* 1.3 86.7 + - - +
200B ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ALA 5.6 0.2 - - - -
108B ILE 4.4 0.2 - - - -
109B HIS* 2.7 17.7 + - - -
110B VAL* 2.6 25.9 + - + +
124B VAL* 4.3 13.2 - - + -
190B GLN* 3.3 28.5 - - + +
192B ILE* 3.3 21.0 - - + +
197B ASN* 4.9 1.3 - - - +
199B SER* 1.3 74.5 - - - +
201B THR* 1.3 63.8 + - - +
202B ILE* 6.1 0.7 - - + -
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Residues in contact with THR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.5 8.5 - - + +
16B ILE* 5.0 14.1 - - + -
28B VAL* 4.5 5.4 - - - +
29B ALA 5.3 0.5 + - - -
31B ALA* 3.2 22.7 + - + +
32B ILE 3.2 13.9 + - - -
107B THR* 4.3 13.7 - - + -
108B ILE 3.1 13.2 - - - +
109B HIS* 3.1 26.6 + - + +
190B GLN* 2.6 19.1 + - - +
200B ALA* 1.3 79.3 + - - +
202B ILE* 1.3 74.4 + - - +
203B ILE* 5.4 1.6 - - + -
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 3.2 23.1 - - + +
34B ALA* 4.7 4.0 - - + +
106B TYR 3.7 1.0 - - - +
107B THR* 3.4 2.8 - - - +
108B ILE* 2.7 50.3 + - + +
124B VAL* 4.6 9.9 - - + +
126B LEU* 4.4 28.3 - - + +
188B PRO* 3.9 35.2 - - + +
189B HIS* 4.0 11.7 - - - +
190B GLN* 4.6 5.8 - - + +
200B ALA* 6.1 0.4 - - + -
201B THR* 1.3 85.8 - - - +
203B ILE* 1.3 73.0 + - - +
204B ALA* 4.9 1.1 - - + -
223B LEU* 6.4 0.7 - - + -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG* 4.8 4.5 - - - +
31B ALA* 4.4 9.4 - - + -
32B ILE 2.9 31.4 + - - +
33B VAL* 3.7 19.7 - - + +
34B ALA* 2.7 32.0 + - - +
38B TRP* 4.8 15.0 - - + +
39B PRO* 4.0 16.4 - - + -
106B TYR 3.3 2.0 - - - -
107B THR* 3.6 14.1 - - + +
201B THR* 5.4 1.6 - - + -
202B ILE* 1.3 77.3 - - - +
204B ALA* 1.3 59.5 + - - +
205B PRO* 3.9 1.8 - - - +
249B MET* 3.6 28.0 - - + -
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ALA* 3.3 10.8 - - + -
39B PRO* 3.6 6.1 - - - +
105B GLY* 2.6 34.1 - - - -
106B TYR* 2.6 25.2 + - + +
108B ILE* 5.6 0.9 - - + -
126B LEU* 3.9 26.7 - - + -
202B ILE* 4.9 1.3 - - + -
203B ILE* 1.3 74.8 - - - +
205B PRO* 1.3 59.3 - - + +
221B TRP* 3.9 15.0 - - + +
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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