Contacts of the strand formed by residues 154 - 159 (chain C) in PDB entry 4K9N
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 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU 2.9 15.4 + - - +
93C ILE* 3.9 12.1 - - + -
94C VAL* 2.9 31.1 + - - +
123C VAL* 4.2 3.8 - - - +
124C LYS* 4.2 3.4 - - + -
125C TRP* 3.3 24.5 - - + +
142C ALA* 3.4 31.9 - - + +
145C MET* 3.8 16.6 - - + -
146C ALA* 3.6 26.5 - - + +
152C GLY 4.0 0.7 - - - +
153C PRO* 1.3 79.5 - - - +
155C TYR* 1.3 61.7 + - - +
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Residues in contact with TYR 155 (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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75C THR* 2.8 44.5 + - + +
82C LEU* 5.8 1.3 - - + -
94C VAL* 3.2 29.2 - - + -
96C ALA* 3.4 18.5 - - + +
112C ASN* 3.0 21.5 + - - -
115C ALA 3.6 22.4 - - - -
116C ALA* 4.7 1.8 - - - -
118C LEU* 4.4 0.3 - - - +
119C PRO* 3.5 20.4 - - + -
123C VAL* 4.4 5.8 - - + -
125C TRP* 2.9 12.2 + - - +
126C SER* 3.3 27.8 - - - +
127C TYR* 3.0 27.2 + - - +
154C VAL* 1.3 77.0 - - - +
156C LEU* 1.3 64.3 + - - +
157C SER* 4.3 13.6 - - - -
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Residues in contact with LEU 156 (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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93C ILE* 5.8 0.2 - - + -
94C VAL 2.8 11.7 + - - +
95C THR* 3.1 10.6 - - + -
96C ALA 2.9 25.5 + - - +
125C TRP* 4.6 2.5 - - + -
127C TYR* 3.4 22.9 - - + +
129C PRO* 3.9 12.6 - - + -
135C VAL* 4.7 3.1 - - + +
138C ALA* 3.7 26.9 - - + +
139C MET* 3.8 51.8 - - + +
142C ALA* 4.7 10.8 - - + -
155C TYR* 1.3 77.7 - - - +
157C SER* 1.3 60.2 + - - +
158C VAL* 4.0 16.4 + - + +
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Residues in contact with SER 157 (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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96C ALA 3.4 7.5 + - - +
98C GLN* 3.6 11.3 + - - +
112C ASN* 4.6 3.3 + - - -
115C ALA* 3.7 20.5 - - - +
127C TYR 2.9 13.6 + - - -
128C GLU* 2.7 34.4 + - - +
129C PRO* 3.0 26.5 - - - +
155C TYR* 4.3 13.1 - - - -
156C LEU* 1.3 73.2 - - - +
158C VAL* 1.3 60.2 + - - +
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Residues in contact with VAL 158 (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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95C THR* 5.6 3.8 - - - -
96C ALA 3.0 10.8 + - - +
97C GLY* 3.7 5.6 - - - -
98C GLN* 3.0 18.4 + - - -
129C PRO* 4.9 1.1 - - + -
135C VAL* 3.9 29.4 - - + -
139C MET* 5.4 1.1 - - + -
156C LEU* 4.0 28.3 - - + +
157C SER* 1.3 79.7 + - - +
159C PRO* 1.3 78.2 - - - +
160C TYR* 3.4 2.4 + - - -
162C ASP* 3.9 4.5 - - + +
163C TRP* 3.5 41.2 + - + -
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Residues in contact with PRO 159 (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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98C GLN* 3.6 17.9 - - + +
99C GLN 3.3 19.3 - - - +
101C ARG* 3.7 35.9 - - + +
104C ILE* 4.3 5.8 - - + -
128C GLU* 4.3 8.5 - - + +
129C PRO* 5.0 1.8 - - + -
157C SER 4.0 5.6 - - - +
158C VAL* 1.3 87.9 - - + +
160C TYR* 1.3 66.1 + - - +
161C ASP* 3.1 13.2 - - - +
162C ASP* 3.0 35.7 + - - +
163C TRP* 4.3 0.3 + - - -
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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