Contacts of the strand formed by residues 154 - 163 (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 PRO 154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C LYS* 2.9 29.1 - - - +
91C SER* 3.0 21.4 - - - -
92C MET* 4.5 10.8 - - + +
95C MET* 4.5 7.6 - - - -
96C LEU* 4.0 17.0 - - + -
147C ASP 3.8 6.3 - - - +
153C GLU* 1.3 84.8 - - + +
155C GLN* 1.3 58.8 + - - +
234C PHE* 3.7 30.5 - - + -
277C TRP* 3.6 31.2 - - + +
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Residues in contact with GLN 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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1C MET* 4.8 9.1 - - - +
85C SER* 4.0 29.9 + - - -
86C ALA 4.7 7.9 - - - +
88C LYS* 4.9 7.9 - - + +
91C SER* 3.5 1.8 - - - -
95C MET* 4.6 0.2 - - - -
147C ASP* 3.1 15.8 + - - -
149C SER* 3.8 37.5 - - - +
153C GLU 2.9 6.6 + - - -
154C PRO* 1.3 73.3 - - - +
156C LEU* 1.3 55.1 + - - +
157C HIS* 2.5 46.4 + - - +
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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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26C LEU* 3.7 27.8 - - + -
85C SER* 3.8 0.3 - - - -
86C ALA* 3.0 31.2 + - + +
90C VAL* 5.0 5.6 - - + -
91C SER* 2.7 21.3 + - - +
94C ALA* 4.4 12.1 - - + -
95C MET* 3.7 12.7 - - + +
102C LEU 5.1 0.2 - - - +
103C ILE* 4.3 22.9 - - + -
106C HIS* 3.6 36.3 - - + +
145C ASN* 4.9 3.8 - - + +
146C HIS 3.5 18.2 - - - +
155C GLN* 1.3 72.0 - - - +
157C HIS* 1.3 67.6 + - - +
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Residues in contact with HIS 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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83C THR* 4.0 10.8 - - + -
84C PHE 3.0 18.2 - - - +
85C SER* 3.7 11.9 - - - +
106C HIS* 3.5 5.9 - - - -
145C ASN* 3.2 8.0 - - - +
146C HIS* 3.1 40.4 + - + +
148C THR 3.4 22.6 + - - -
155C GLN* 2.5 46.5 + - - -
156C LEU* 1.3 77.5 - - - +
158C THR* 1.3 65.0 + - - +
159C HIS* 3.3 19.3 - + - -
902C MG 2.8 29.3 - - - -
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Residues in contact with THR 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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32C ARG* 4.7 1.9 + - - +
82C LEU 3.5 3.1 - - - +
83C THR* 3.4 2.7 - - - -
84C PHE* 2.9 30.3 + - - +
106C HIS* 2.8 29.9 + - - -
107C ASN* 4.2 1.4 + - - -
110C VAL* 3.7 25.2 - - + +
143C LEU* 3.5 28.7 - - + -
144C PHE 2.9 11.9 - - - +
145C ASN* 3.1 18.1 + - - +
157C HIS* 1.3 73.9 + - - +
159C HIS* 1.3 66.3 + - - +
160C ALA* 4.4 1.1 - - + +
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Residues in contact with HIS 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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16C TYR* 4.4 15.0 - + - -
17C TYR* 4.2 6.8 - + + -
81C ASP* 3.5 27.0 + - - +
82C LEU 3.9 2.2 - - - -
83C THR* 3.5 19.7 + - + +
142C ALA 3.2 13.5 - - - +
143C LEU* 3.3 0.3 - - - -
144C PHE* 2.7 27.1 + - + +
146C HIS* 3.3 29.7 + + - -
157C HIS* 3.3 16.2 - + - -
158C THR* 1.3 70.5 - - - +
160C ALA* 1.3 60.4 + - - +
161C VAL* 3.0 16.7 + - + +
902C MG 2.1 32.1 - - - -
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Residues in contact with ALA 160 (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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82C LEU* 2.7 49.0 + - + +
84C PHE* 4.1 5.6 - - + -
110C VAL* 5.2 1.8 - - + -
114C VAL* 3.8 21.1 - - + -
141C MET* 5.1 0.2 - - - -
143C LEU* 3.7 25.6 - - + -
158C THR 3.6 1.8 + - - -
159C HIS* 1.3 69.1 - - - +
161C VAL* 1.3 58.5 + - - +
162C VAL* 3.1 19.4 + - + +
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Residues in contact with VAL 161 (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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7C VAL* 3.7 26.9 - - + -
17C TYR* 3.3 38.6 - - + +
52C PHE* 3.4 29.0 - - + -
56C LEU* 4.3 4.9 - - + -
80C TYR 3.4 4.3 - - - -
81C ASP* 4.5 1.8 - - - +
140C VAL 3.8 0.5 - - - +
141C MET* 3.3 5.8 - - - -
142C ALA* 3.1 39.4 + - - +
144C PHE* 3.7 4.3 - - + -
159C HIS* 3.0 13.4 + - + +
160C ALA* 1.3 68.1 - - - +
162C VAL* 1.3 59.1 + - - +
163C ALA 3.4 4.9 + - - +
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Residues in contact with VAL 162 (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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79C GLY* 3.7 0.2 - - - -
80C TYR* 2.8 35.7 + - + +
82C LEU* 4.1 24.2 - - + -
117C VAL* 5.2 1.6 - - + -
139C LEU* 3.7 37.5 - - + -
141C MET* 3.8 28.0 - - + -
160C ALA* 3.4 14.8 - - + +
161C VAL* 1.3 67.4 - - - +
163C ALA* 1.3 73.1 + - - +
164C ASN* 3.4 1.2 + - - -
175C LEU* 4.0 7.0 - - + +
185C PHE* 4.4 9.9 - - + -
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Residues in contact with ALA 163 (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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52C PHE* 5.3 1.1 - - + -
55C LEU* 3.7 33.9 - - + +
56C LEU* 4.7 13.2 - - + -
78C PRO 4.0 5.4 - - - -
79C GLY* 4.4 1.8 - - - -
140C VAL 3.1 23.0 + - - +
161C VAL* 3.4 4.8 + - - +
162C VAL* 1.3 80.5 - - - +
164C ASN* 1.3 58.9 + - - +
165C VAL* 2.8 24.2 + - + +
175C LEU* 3.1 10.7 - - - +
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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