Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 3M4D
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 LYS 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLN* 6.5 0.7 - - - -
88A LEU 3.3 9.2 - - - +
89A GLN* 4.1 30.4 - - + +
98A ILE* 3.3 3.7 - - - +
159A SER 5.3 4.0 - - - +
160A PRO* 3.4 2.6 - - - +
161A THR* 2.9 58.6 + - + +
163A LYS* 1.3 83.0 - - + +
165A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLN* 3.4 2.9 - - - +
88A LEU* 2.9 39.6 + - + +
98A ILE* 3.6 22.0 - - + -
101A TYR* 3.9 28.5 - - + -
157A LEU* 4.0 18.8 - - + -
159A SER 5.5 0.7 - - - -
160A PRO* 4.0 12.6 - - + -
164A LYS* 1.3 76.4 - - - +
166A GLY* 1.3 64.0 + - - +
167A TRP* 4.2 5.4 - - + -
230A THR* 3.8 28.0 - - + +
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL 3.1 12.8 - - - -
87A GLN* 4.0 8.3 - - - -
157A LEU* 3.6 8.7 - - - +
158A GLU* 2.8 37.2 + - - +
159A SER 5.8 0.2 + - - -
165A VAL* 1.3 79.8 - - - +
167A TRP* 1.3 69.3 + - - -
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Residues in contact with TRP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR* 4.7 1.6 - - - -
84A PHE 4.6 0.2 - - - -
85A LYS* 3.3 6.4 - - - +
86A VAL* 2.9 34.6 + - + +
87A GLN* 5.1 1.2 - - - +
88A LEU* 3.8 16.4 - - + -
101A TYR* 3.8 18.8 - - + -
102A TYR 3.7 10.8 - - - -
103A PRO* 2.8 32.5 + - + +
155A THR* 4.7 3.8 - - + -
156A ILE 3.2 17.3 - - - +
157A LEU* 3.5 15.4 - - + +
158A GLU* 4.2 4.0 - - - +
165A VAL* 4.2 9.0 - - + -
166A GLY* 1.3 77.0 - - - -
168A LYS* 1.3 62.1 + - - +
169A VAL* 5.6 0.2 - - - -
228A PHE* 3.6 61.7 - + + -
229A ALA 3.3 26.2 - - - -
230A THR* 3.4 18.2 - - - -
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Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA* 5.6 0.2 - - + -
84A PHE 3.3 5.4 - - - +
85A LYS* 3.9 21.3 - - + +
154A LYS 3.5 2.4 - - - +
156A ILE* 2.9 65.3 + - + +
158A GLU* 3.7 34.3 + - + +
167A TRP* 1.3 76.9 - - - +
169A VAL* 1.3 62.6 + - - +
170A ILE* 3.7 18.0 + - + +
213B PRO* 6.0 2.2 - - - +
214B ASN* 3.3 22.5 + - - +
221B SER* 5.7 2.6 + - - -
222B SER* 4.3 5.6 + - - -
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.4 2.4 - - - -
84A PHE* 2.8 43.5 + - + +
153A PHE* 3.8 31.5 - - + -
154A LYS 3.2 7.0 - - - +
155A THR* 4.0 14.4 - - + +
168A LYS* 1.3 75.2 - - - +
170A ILE* 1.3 61.1 + - - +
219A LEU* 4.4 2.0 - - + -
224A PHE* 3.4 40.4 - - + -
228A PHE* 4.1 12.6 - - + -
107G ILE* 4.2 13.9 - - + -
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Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A SER 3.5 5.6 - - - +
83A ALA* 4.1 16.2 - - + -
85A LYS* 5.9 0.2 - - - -
153A PHE* 3.1 6.9 - - - -
154A LYS* 2.9 47.8 + - + +
156A ILE* 3.7 16.6 - - + -
168A LYS* 3.8 28.9 - - + -
169A VAL* 1.3 73.7 - - - +
171A PHE* 1.3 71.4 + - - +
172A ASN* 3.2 0.6 + - - -
214B ASN* 3.0 57.0 - - + +
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TRP* 3.5 39.0 - + + -
82A SER* 2.8 20.5 + - - +
152A ASP* 3.8 7.2 - - + -
153A PHE* 3.3 31.1 - + + -
170A ILE* 1.3 79.8 - - - +
172A ASN* 1.3 73.0 + - - +
173A ASN* 3.7 10.5 - - - -
174A MET* 3.7 41.1 - - + -
183A ASP* 4.0 14.8 - - - -
184A ARG* 4.2 15.3 + - + +
195A LEU* 3.9 19.3 - - + -
196A PHE* 4.7 4.9 - + - -
220A LEU* 4.4 3.1 - - + -
214B ASN* 5.7 1.2 + - - +
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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