Contacts of the strand formed by residues 165 - 170 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU 5.1 0.2 - - - -
115A LEU* 3.7 27.8 - - + -
135A HIS* 4.7 1.1 - - + -
136A GLY 4.0 2.9 - - - -
137A ALA* 4.2 1.8 - - + -
32D HIS* 3.5 24.2 - + + -
33D LEU 3.2 15.7 - - - +
34D ILE* 3.6 4.9 - - + -
45D TRP* 3.9 6.4 - - - -
76D TYR* 3.7 24.5 - + - -
77D SER* 2.7 25.6 + - - -
78D GLN* 3.0 60.9 + - + +
134D TYR* 3.9 13.0 - + - -
161D PRO 3.7 16.8 - - - -
162D SER 3.9 7.4 - - - -
164D VAL* 1.3 78.9 - - - +
166D PHE* 1.3 58.1 + - - +
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Residues in contact with PHE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D HIS* 4.8 0.2 - - - -
33D LEU* 2.7 65.1 + - + +
45D TRP* 3.7 38.4 - + + -
65D LEU* 4.3 9.6 - - + -
75D VAL* 4.0 13.0 - - + -
76D TYR* 3.3 15.5 - - - -
77D SER* 3.8 7.0 - - - +
101D VAL* 3.8 21.3 - - + -
147D LEU* 3.7 41.7 - - + -
148D SER* 4.2 2.9 - - - -
149D THR* 3.8 19.3 - - + -
165D PHE* 1.3 82.2 - - - +
167D GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ALA 3.2 14.8 - - - -
32D HIS* 4.2 0.4 - - - -
65D LEU* 4.9 4.9 - - - -
75D VAL* 3.5 3.8 - - - +
76D TYR* 2.9 53.2 + - - +
166D PHE* 1.3 79.5 - - - +
168D ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ALA* 5.6 0.6 - - - +
30D ALA* 3.2 2.6 - - - +
31D ALA 2.7 38.4 + - - +
58D PHE* 3.8 20.3 - - + -
65D LEU* 4.3 5.8 - - + +
73D TYR* 4.8 4.3 - - + -
74D PHE 3.2 12.6 - - - +
75D VAL* 4.1 15.5 - - + -
76D TYR* 4.1 2.0 - - - -
147D LEU* 4.2 13.9 - - + -
167D GLY* 1.3 75.6 - - - +
169D PHE* 1.3 63.5 + - - +
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Residues in contact with PHE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.4 36.6 - + + -
138A ALA* 4.3 6.1 - - + -
169A PHE* 4.9 1.6 - + - -
171A LEU* 3.4 44.6 - - + -
169B PHE* 4.5 11.2 - + - -
29D PRO 3.6 11.4 - - - +
30D ALA* 3.9 5.2 - - + +
73D TYR* 3.3 6.8 - - - -
74D PHE* 3.0 69.4 + + + -
76D TYR* 4.3 9.9 - + - -
168D ALA* 1.3 78.7 - - - +
170D ALA* 1.3 73.6 + - - +
171D LEU* 3.6 13.6 + - + -
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 5.3 5.0 - - - +
28D LYS* 4.9 11.3 - - + +
29D PRO* 3.1 39.2 + - + +
69D THR* 6.0 1.3 - - + -
72D ILE 3.7 3.6 - - - +
73D TYR* 3.4 27.8 - - + +
169D PHE* 1.3 83.7 - - - +
171D LEU* 1.3 67.0 + - - +
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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