Contacts of the strand formed by residues 125 - 134 (chain C) in PDB entry 2PQA
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 TYR 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C VAL* 4.1 14.4 - - + -
78C GLY* 3.5 26.2 - - - -
79C ILE* 4.0 31.1 - - + +
95C ASP 5.1 0.4 - - - -
96C ASP* 6.0 1.6 - - - -
97C MET* 4.5 5.2 - - + +
123C GLU 4.2 0.4 + - - -
124C THR* 1.3 79.0 - - - +
126C VAL* 1.3 63.0 + - - +
148C PRO* 3.5 2.1 - - - +
149C LEU* 3.1 26.4 + - + +
152C MET* 3.5 37.7 - - + -
155C PHE* 4.1 18.4 - + - -
11D ARG* 4.0 6.9 + - - -
68D GLU* 2.5 39.8 + - - -
85D VAL* 4.8 7.4 - - + -
87D PHE* 3.8 14.8 - + - -
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Residues in contact with VAL 126 (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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76C ILE 3.8 0.7 - - - +
77C VAL* 3.3 6.6 - - - +
78C GLY 2.9 39.5 + - - +
80C ILE* 3.9 29.6 - - + -
94C ILE* 3.8 30.1 - - + -
120C VAL* 4.2 11.2 - - + -
124C THR* 4.3 0.9 - - + +
125C TYR* 1.3 81.2 - - - +
127C LYS* 1.3 59.8 + - - +
128C VAL* 4.1 5.8 - - + -
146C ILE* 4.1 17.9 - - + -
147C MET 3.6 5.4 - - - +
148C PRO* 4.0 14.6 - - + -
149C LEU* 4.2 5.8 - - - -
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Residues in contact with LYS 127 (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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161A GLU* 4.7 16.6 + - - +
75C THR* 3.3 30.1 - - - +
76C ILE 3.5 2.9 - - - -
77C VAL* 3.9 15.7 - - + -
126C VAL* 1.3 74.5 - - - +
128C VAL* 1.3 62.0 + - - +
145C LYS 3.9 0.2 - - - +
146C ILE* 3.5 2.9 - - - -
147C MET* 2.9 62.6 + - + +
149C LEU* 3.6 15.9 - - + +
154C GLU* 3.5 27.6 + - + +
158C HIS* 4.5 11.7 - - - +
161C GLU* 4.9 7.3 + - - -
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL 4.0 0.2 - - - +
75C THR* 3.1 9.7 + - - -
76C ILE* 2.9 42.0 + - + +
94C ILE* 3.6 30.1 - - + -
104C VAL* 4.0 10.8 - - + -
126C VAL* 4.1 5.2 - - + +
127C LYS* 1.3 80.5 - - - +
129C ALA* 1.3 67.6 + - - +
141C LEU* 4.6 13.9 - - + +
143C ALA* 3.9 21.1 - - + -
145C LYS 3.3 8.3 - - - +
146C ILE* 3.8 21.5 - - + -
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Residues in contact with ALA 129 (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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46C ILE* 5.2 14.4 - - + -
74C VAL 3.5 8.7 - - - +
75C THR* 4.5 7.0 - - - +
128C VAL* 1.3 77.7 - - - +
130C GLY* 1.3 58.2 + - - +
143C ALA* 3.6 1.9 - - - -
144C PHE* 2.8 26.4 + - + -
145C LYS* 3.0 30.6 + - + +
147C MET* 4.7 9.2 - - + +
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Residues in contact with GLY 130 (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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72C SER 3.8 0.5 - - - +
73C GLN* 3.6 2.4 - - - +
74C VAL* 3.1 35.3 + - - +
128C VAL* 4.7 0.8 - - - +
129C ALA* 1.3 74.7 - - - +
131C HIS* 1.3 66.9 + - - -
141C LEU* 4.9 7.8 - - - +
142C VAL 3.0 14.6 - - - -
143C ALA* 4.0 2.2 - - - -
144C PHE* 4.0 10.1 - - - -
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Residues in contact with HIS 131 (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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72C SER* 3.5 15.9 + - - +
73C GLN* 3.2 40.4 + - + +
130C GLY* 1.3 78.1 - - - -
132C LEU* 1.3 64.0 + - - +
133C ARG* 3.4 32.9 + - - +
141C LEU* 3.5 4.1 - - - -
142C VAL* 2.7 47.6 + - + +
144C PHE* 3.6 31.4 - + - -
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Residues in contact with LEU 132 (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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54C LEU* 3.8 44.9 - - + +
57C ALA* 4.3 12.1 - - + -
64C PHE* 3.4 59.4 - - + -
71C ILE* 5.0 4.3 - - + -
72C SER* 3.2 18.7 + - - +
74C VAL* 4.9 1.8 - - + +
102C MET* 4.6 2.0 - - + -
130C GLY 4.2 0.2 + - - -
131C HIS* 1.3 72.8 - - - +
133C ARG* 1.3 74.5 + - - +
139C LYS* 4.5 11.9 - - + -
140C SER 3.7 9.6 - - - +
141C LEU* 3.8 17.2 - - + +
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Residues in contact with ARG 133 (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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64C PHE* 4.3 3.9 - - - -
72C SER* 5.1 4.0 + - - -
131C HIS* 3.4 37.1 + - - +
132C LEU* 1.3 83.9 + - - +
134C SER* 1.3 61.3 + - - +
138C LYS 4.5 0.2 - - - -
139C LYS* 3.5 5.5 - - - +
140C SER* 2.8 41.7 + - - +
142C VAL* 4.0 30.0 - - + +
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Residues in contact with SER 134 (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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59C LEU* 4.5 14.0 - - - +
64C PHE* 3.5 26.6 - - - -
133C ARG* 1.3 78.6 - - - +
135C PHE* 1.3 63.3 + - - +
137C ASN* 4.1 19.6 + - - -
138C LYS 3.2 10.6 + - - -
139C LYS* 4.3 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