Contacts of the strand formed by residues 79 - 85 (chain C) in PDB entry 1P4D
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 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A ILE* 4.8 0.2 - - - +
6C GLN* 3.8 5.9 - - - +
7C VAL* 2.8 29.5 + - - +
56C LEU* 5.4 0.4 - - - -
77C ARG 3.6 1.6 + - - -
78C PRO* 1.3 83.3 - - - +
80C TYR* 1.3 74.1 + - - -
162C VAL 3.7 12.1 - - - -
163C ALA* 4.3 2.2 - - - -
164C ASN* 3.7 9.6 - - - -
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Residues in contact with TYR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASP* 4.5 9.6 - - - -
271A GLU* 3.6 8.5 + - - -
272A ILE* 4.2 17.7 - - + -
5C ALA 3.6 5.8 - - - +
7C VAL* 3.0 10.9 - - - +
77C ARG* 5.7 1.8 - - + -
79C GLY* 1.3 85.2 - - - -
81C ASP* 1.3 60.5 + - - +
82C LEU* 3.9 10.8 - - + -
160C ALA 3.6 0.6 - - - +
161C VAL* 3.4 0.7 - - - -
162C VAL* 2.8 44.3 + - + +
164C ASN* 4.8 6.5 - - + -
175C LEU* 4.3 9.2 + - + -
176C SER* 3.6 30.7 + - - -
185C PHE* 3.1 43.1 - + - -
186C ILE* 3.4 40.0 + - + +
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Residues in contact with ASP 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C SER 3.6 3.3 - - - +
4C ILE* 3.8 0.9 - - - -
5C ALA* 2.7 44.7 + - + +
6C GLN 4.3 4.3 - - - +
7C VAL* 3.6 4.9 - - + +
16C TYR* 5.1 1.9 - - - -
17C TYR* 2.5 36.1 + - - +
80C TYR* 1.3 73.6 - - - +
82C LEU* 1.3 62.0 + - - +
83C THR* 2.9 27.2 + - - -
159C HIS* 3.5 21.0 + - - +
160C ALA 4.0 1.8 - - - -
161C VAL* 4.5 2.9 - - - +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C MET* 3.9 32.3 - - + -
3C SER 3.7 2.5 - - - -
4C ILE* 3.9 21.1 - - + -
80C TYR* 4.7 6.7 - - + -
81C ASP* 1.3 80.6 + - - +
83C THR* 1.3 56.0 + - - +
84C PHE* 3.4 17.9 - - + -
114C VAL* 5.8 1.3 - - + -
117C VAL* 3.7 31.2 - - + -
160C ALA* 2.7 53.3 + - + +
162C VAL* 4.1 16.2 - - + -
185C PHE* 5.7 0.9 - - + -
186C ILE* 5.4 0.4 - - + -
189C VAL* 4.1 12.3 - - + -
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Residues in contact with THR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 3.2 4.9 - - - +
2C MET* 3.2 1.6 - - - -
3C SER* 3.0 48.8 + - - +
5C ALA* 6.0 0.5 - - - +
81C ASP* 2.9 20.2 + - - -
82C LEU* 1.3 70.3 - - - +
84C PHE* 1.3 63.1 + - - +
85C SER* 3.9 12.7 + - - +
155C GLN* 6.0 0.2 - - - +
157C HIS* 4.0 26.7 - - + -
158C THR 3.4 9.0 - - - +
159C HIS* 3.5 16.7 + - + +
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 3.3 3.8 - - - -
2C MET* 3.5 43.5 - - + -
82C LEU* 3.4 25.1 - - + -
83C THR* 1.3 72.5 - - - +
85C SER* 1.3 61.6 + - - +
106C HIS* 3.7 3.3 + - - -
110C VAL* 4.1 26.7 - - + -
113C ALA* 3.7 30.1 - - + -
114C VAL* 4.1 12.1 - - + -
117C VAL* 4.8 5.8 - - + -
157C HIS* 3.0 6.8 - - - +
158C THR 2.9 35.1 + - - +
160C ALA* 4.1 11.9 - - + -
196C PHE 4.5 3.6 - - - -
200C TYR* 3.8 32.5 - + + -
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.0 49.2 + - - +
3C SER* 5.3 1.2 + - - -
83C THR* 4.2 10.7 + - - +
84C PHE* 1.3 74.6 - - - +
86C ALA* 1.3 63.3 + - - +
87C PRO* 4.3 0.9 - - - +
155C GLN* 4.0 26.9 + - - -
157C HIS* 3.7 10.4 - - - +
200C TYR* 3.2 19.6 - - - -
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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