Contacts of the strand formed by residues 165 - 170 (chain A) in PDB entry 4MXV
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 PHE 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 3.5 28.3 - + + +
33A LEU 3.1 16.4 - - - +
34A ILE* 4.9 0.9 - - + -
45A TRP* 3.7 6.0 - - - -
76A TYR* 3.6 28.7 - + - -
77A SER* 2.7 25.6 + - - -
78A GLN* 2.8 64.4 + - + +
134A TYR* 3.9 3.6 - + - -
161A PRO 3.8 17.0 - - - +
162A SER* 3.8 9.6 - - - -
164A VAL* 1.3 80.8 - - - +
166A PHE* 1.3 55.6 + - - +
114B LEU 5.4 0.2 - - - -
115B LEU* 4.0 19.5 - - + -
135B HIS* 5.0 0.2 - - + -
136B GLY 3.7 14.8 - - - -
137B ALA* 3.9 1.6 - - + -
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Residues in contact with PHE 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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32A HIS* 3.7 0.7 + - - -
33A LEU* 2.5 64.5 + - + +
45A TRP* 3.6 39.5 - + + -
63A ASN 5.4 0.4 - - - -
64A SER 5.4 0.2 - - - -
65A LEU* 4.4 9.4 - - + -
75A VAL* 4.3 10.3 - - + -
76A TYR* 3.6 13.9 - - - -
77A SER* 3.9 4.0 - - - +
101A VAL* 3.7 21.5 - - + -
147A LEU* 3.7 42.4 - - + -
148A SER* 4.0 8.3 - - - -
149A THR* 4.0 18.6 - - + -
165A PHE* 1.3 74.7 - - - +
167A GLY* 1.3 67.8 + - - +
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Residues in contact with GLY 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA 3.2 13.5 - - - -
32A HIS* 4.2 0.2 - - - -
65A LEU* 4.8 4.9 - - - -
75A VAL* 3.5 3.8 - - - +
76A TYR* 2.9 54.1 + - - +
166A PHE* 1.3 80.0 - - - +
168A ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 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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30A ALA* 3.4 1.2 - - - -
31A ALA 2.8 32.7 + - - +
58A PHE* 3.8 13.3 - - + -
65A LEU* 4.0 20.9 - - + +
73A TYR* 4.9 3.8 - - + -
74A PHE 3.2 11.0 - - - +
75A VAL* 3.8 17.5 - - + -
76A TYR* 3.8 1.9 - - - -
147A LEU* 4.2 6.7 - - + -
167A GLY* 1.3 76.2 - - - +
169A PHE* 1.3 65.4 + - - +
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Residues in contact with PHE 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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29A PRO 3.7 4.0 - - - +
30A ALA* 3.7 11.9 - - + +
58A PHE* 4.7 0.2 - - - -
73A TYR* 3.2 10.1 - - - -
74A PHE* 3.0 66.9 + + + -
76A TYR* 4.2 12.8 - + - -
168A ALA* 1.3 78.5 - - - +
170A ALA* 1.3 73.4 + - - +
171A LEU* 3.8 19.7 - - + -
74B PHE* 3.9 27.1 - + + -
138B ALA* 4.4 6.5 - - + -
169B PHE* 4.6 10.1 - + - -
171B LEU* 3.4 49.1 - - + -
169D PHE* 4.9 1.6 - + - -
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Residues in contact with ALA 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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28A LYS* 4.1 17.8 - - + +
29A PRO* 3.0 41.2 + - + +
72A ILE 3.7 1.8 - - - +
73A TYR* 3.7 24.1 - - + -
169A PHE* 1.3 85.0 - - - +
171A LEU* 1.3 64.8 + - - +
171B LEU* 5.0 4.0 - - - +
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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