Contacts of the strand formed by residues 94 - 101 (chain C) in PDB entry 4IRQ
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 ARG 94 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ASP* 5.1 1.0 + - - -
84C TRP* 3.4 45.8 - - + +
86C GLU* 3.0 36.8 + - - -
92C PRO 3.6 12.5 + - - +
93C HIS* 1.3 72.5 - - - +
95C LEU* 1.3 60.2 + - - +
96C ALA 3.9 0.3 + - - -
125C ARG* 3.5 21.8 - - + +
155C SER* 3.6 34.8 + - - +
156C THR* 3.9 0.7 - - - +
157C ASP* 2.9 37.0 + - - +
158C TYR* 3.2 12.8 + - - +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C TRP* 3.3 4.2 - - - -
94C ARG* 1.3 71.4 - - - +
96C ALA* 1.3 62.6 + - - +
97C VAL* 3.9 20.2 - - + -
119C LEU* 4.1 16.6 - - + -
124C ILE* 3.8 17.5 - - + -
125C ARG 2.8 16.6 + - - +
126C HIS* 3.1 2.8 - - + +
127C HIS 3.0 25.5 + - - -
158C TYR* 3.4 33.3 - - + +
159C ILE 3.6 6.3 - - - -
160C ALA* 3.3 36.1 - - + +
175C TYR* 4.2 17.3 - - + +
205C LEU* 4.9 0.9 - - + -
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C TRP* 4.5 2.9 - - + -
94C ARG 3.9 0.8 + - - -
95C LEU* 1.3 72.7 - - - +
97C VAL* 1.3 61.9 + - - +
98C LEU* 3.4 4.6 + - + +
127C HIS 3.6 4.7 - - - -
129C TYR* 4.0 19.3 - - + -
152C SER* 4.2 6.3 - - - -
156C THR* 3.6 30.3 - - + +
158C TYR 2.8 10.0 + - - +
159C ILE* 3.3 12.5 - - + +
160C ALA 2.9 24.4 + - - -
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 3.9 19.1 - - + +
96C ALA* 1.3 70.3 - - - +
98C LEU* 1.3 58.6 + - - +
99C VAL* 3.6 20.0 + - + +
111C PHE* 4.5 7.0 - - + -
115C MET* 5.4 4.7 - - + -
119C LEU* 3.8 28.5 - - + -
126C HIS* 4.7 1.6 - - + -
127C HIS 2.8 18.1 + - - +
128C ILE* 4.0 16.6 - - + -
129C TYR* 2.7 34.3 + - - +
160C ALA* 3.7 5.8 - - + +
162C HIS* 4.0 22.7 - - + -
175C TYR* 6.1 0.9 - - + -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ALA* 3.9 16.2 - - + +
97C VAL* 1.3 70.6 - - - +
99C VAL* 1.3 60.9 + - - +
100C PRO* 3.3 6.0 - - - +
129C TYR* 3.8 26.7 - - + -
131C LEU* 3.8 11.4 - - + -
145C ILE* 3.9 24.7 - - + +
148C GLY* 3.6 25.8 - - - +
149C PHE* 3.8 20.2 - - + +
152C SER* 4.5 0.4 - - - -
159C ILE* 3.7 30.5 - - + -
160C ALA 2.7 14.2 + - - +
161C MET* 3.8 1.6 - - - -
162C HIS 3.0 25.2 + - - -
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C VAL* 3.8 15.7 - - + -
98C LEU* 1.3 74.2 - - - +
100C PRO* 1.3 68.7 - - - +
101C PHE* 3.3 6.0 + - + +
108C LEU* 5.4 0.2 - - + -
111C PHE* 3.7 25.1 - - + -
128C ILE* 3.9 8.5 - - + -
129C TYR 2.8 20.2 + - - +
130C VAL* 3.7 9.3 - - + -
131C LEU* 2.8 31.4 + - - +
162C HIS 3.6 14.4 - - - +
164C VAL* 3.6 35.7 - - + -
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Residues in contact with PRO 100 (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 LEU 3.3 11.2 - - - +
99C VAL* 1.3 84.5 - - - +
101C PHE* 1.3 61.3 + - - +
131C LEU* 4.0 7.3 - - + +
139C PHE* 3.9 14.1 - - + -
141C ARG* 3.6 45.8 - - + +
144C LEU* 4.4 5.8 - - + -
145C ILE* 3.9 13.7 - - + -
162C HIS 3.4 14.8 - - - +
163C ASP* 3.9 9.0 - - - +
402C UDP 2.8 31.3 + - - +
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Residues in contact with PHE 101 (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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99C VAL* 3.7 3.1 - - + +
100C PRO* 1.3 74.1 - - - +
102C ARG* 1.3 62.3 + - - +
103C GLU* 3.9 12.6 - - - -
104C ARG* 3.5 47.6 - - + -
105C PHE* 3.9 7.4 - + + -
108C LEU* 3.9 27.6 - - + -
130C VAL* 3.5 33.0 - - + -
131C LEU 2.8 15.7 + - - +
132C ASN* 3.3 22.9 - - - -
133C GLN 2.9 27.9 + - - -
139C PHE* 3.6 9.0 - - - -
164C VAL* 4.1 19.5 - - + -
402C UDP 3.3 2.5 - - - -
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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
------------------------------------------------------------
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