Contacts of the strand formed by residues 108 - 119 (chain D) in PDB entry 3MLQ
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 ILE 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D GLN* 3.5 34.8 - - + +
100D LEU 3.3 5.4 - - - +
101D ILE* 3.4 30.7 - - + -
102D HIS* 5.3 0.4 - - - -
106D GLY 3.5 19.1 - - - +
107D LEU* 1.3 75.5 - - - +
109D LYS* 1.3 64.9 + - - +
110D GLU 4.8 0.2 - - - +
341H ARG* 5.8 4.5 - - + -
343H VAL* 3.8 18.4 - - + -
350H TYR* 3.6 18.8 - - + +
361H LEU* 3.3 10.0 - - - +
362H TYR* 3.1 50.8 + - + -
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Residues in contact with LYS 109 (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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99D GLN* 4.3 1.3 - - - -
100D LEU* 2.6 45.1 + - + +
102D HIS* 5.3 5.2 - - - +
107D LEU* 6.2 0.4 - - + -
108D ILE* 1.3 76.8 - - - +
110D GLU* 1.3 65.3 + - - +
111D ASP* 4.9 0.2 - - - +
367D LEU 5.0 2.5 - - - +
368D THR* 3.8 28.7 - - - +
369D PRO* 3.3 21.0 - - + +
355H TYR* 5.3 6.1 - - - +
358H GLU* 4.2 11.9 - - - +
359H GLY* 3.4 32.5 + - - +
360H LYS 3.8 3.8 - - - +
361H LEU* 3.6 30.6 - - + +
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Residues in contact with GLU 110 (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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87C ASP* 4.7 2.8 - - - +
69D LEU* 3.8 22.4 - - + -
97D ARG* 2.5 46.5 + - - +
98D LEU 3.4 4.0 - - - +
99D GLN* 4.4 8.7 - - + +
108D ILE* 4.3 1.0 - - - +
109D LYS* 1.3 73.9 - - - +
111D ASP* 1.3 58.9 + - - +
112D GLU* 5.3 1.2 - - - +
341H ARG* 4.4 6.3 + - - -
359H GLY* 2.7 34.3 - - - -
360H LYS* 3.3 23.9 + - + +
362H TYR* 3.0 40.6 + - + -
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Residues in contact with ASP 111 (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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130C ASN* 5.4 5.0 + - - -
97D ARG* 3.4 3.8 - - - -
98D LEU* 2.8 40.6 + - - +
109D LYS* 4.9 0.3 - - - -
110D GLU* 1.3 78.8 - - - +
112D GLU* 1.3 71.2 + - - +
113D VAL* 3.5 8.5 + - + +
368D THR* 3.9 15.2 + - - -
369D PRO* 3.9 22.0 - - + +
370D ALA* 4.1 16.4 - - - +
357H GLY 5.2 1.6 - - - +
358H GLU* 3.8 7.2 - - - -
359H GLY* 3.0 28.0 + - - -
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LYS* 3.0 53.1 + - - +
87C ASP* 4.4 14.4 - - + +
88C LEU* 3.6 19.8 - - + +
72D ARG* 4.1 6.6 - - - +
95D TYR* 3.5 37.6 - - + +
96D ALA 3.6 4.2 - - - -
97D ARG* 3.7 23.1 + - + +
110D GLU* 5.3 1.1 - - - +
111D ASP* 1.3 80.1 + - - +
113D VAL* 1.3 62.7 + - - +
114D PHE 3.7 1.0 + - - -
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Residues in contact with VAL 113 (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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95D TYR* 3.6 2.3 - - - -
96D ALA 2.8 35.5 + - - +
98D LEU* 3.8 23.1 - - + -
111D ASP* 4.2 12.8 - - + +
112D GLU* 1.3 72.1 - - - +
114D PHE* 1.3 74.6 + - - +
115D LEU* 3.4 7.4 + - + +
369D PRO 4.2 1.6 - - - -
370D ALA* 3.9 34.1 - - + +
373D VAL* 3.7 31.6 - - + +
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Residues in contact with PHE 114 (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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117C HIS* 6.2 2.2 - + - -
93D PRO* 4.0 20.9 - - + -
94D LEU 3.8 4.9 - - - -
95D TYR* 3.5 39.2 - + + +
112D GLU 3.7 1.2 + - - -
113D VAL* 1.3 78.7 - - - +
115D LEU* 1.3 59.9 + - - +
116D GLY* 3.4 34.5 - - - -
117D HIS* 3.5 25.1 - + - -
375D SER* 3.7 14.0 - - - -
379D GLU* 4.5 9.2 - - - -
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Residues in contact with LEU 115 (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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48D PHE* 3.3 26.7 - - + -
94D LEU* 3.1 29.2 + - + +
96D ALA* 3.2 32.1 - - + +
98D LEU* 5.6 2.5 - - + -
113D VAL* 3.8 11.4 - - + +
114D PHE* 1.3 75.7 - - - +
116D GLY* 1.3 57.7 + - - +
348D LEU* 5.6 0.7 - - + -
351D LEU* 3.9 27.4 - - + -
373D VAL* 3.9 19.5 - - + -
375D SER* 3.1 24.3 + - - +
378D LEU* 4.0 16.6 - - + +
379D GLU* 3.4 9.0 + - - +
382D LEU* 6.2 0.2 - - - +
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Residues in contact with GLY 116 (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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94D LEU* 3.0 30.8 + - - +
114D PHE* 3.4 28.2 - - - -
115D LEU* 1.3 79.6 - - - +
117D HIS* 1.3 60.4 + - - -
118D LEU* 5.2 0.2 - - - +
379D GLU* 3.7 16.4 - - - -
382D LEU* 6.5 1.1 - - - -
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Residues in contact with HIS 117 (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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93C PRO* 6.4 1.6 - - + -
95C TYR* 6.0 2.0 - - - -
114C PHE* 6.3 1.4 - - - -
117C HIS* 5.2 15.8 + + - -
77D PRO* 6.5 1.6 - - + -
91D GLN* 3.7 38.2 + - - +
92D ALA* 3.2 9.1 - - - +
93D PRO* 3.8 26.4 - - + +
114D PHE* 3.5 24.6 - + - -
116D GLY* 1.3 73.4 - - - -
118D LEU* 1.3 62.6 + - - +
119D PRO* 3.4 10.4 - - - +
379D GLU* 4.8 4.6 + - - +
382D LEU* 5.2 8.4 - - - +
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Residues in contact with LEU 118 (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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26D TYR* 4.9 2.9 - - - +
30D LEU* 4.0 17.3 - - + -
44D ILE* 3.4 29.2 - - + -
73D ILE* 3.8 26.5 - - + -
91D GLN* 3.8 1.8 - - - -
92D ALA* 2.7 39.1 + - - +
94D LEU* 4.4 16.6 - - + -
116D GLY 3.9 1.0 + - - +
117D HIS* 1.3 71.5 - - - +
119D PRO* 1.3 68.9 - - + +
120D LEU* 3.5 3.1 + - - +
340D MET* 4.7 14.8 - - + -
344D PHE* 4.2 24.7 - - + -
382D LEU* 4.5 15.7 - - + -
386D PHE* 5.6 1.1 - - + -
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Residues in contact with PRO 119 (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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26D TYR* 2.7 28.2 + - - -
89D THR* 5.0 6.1 - - + -
90D TYR 3.4 14.6 - - - +
91D GLN* 3.6 15.0 - - + +
117D HIS 3.4 10.5 - - - +
118D LEU* 1.3 82.2 - - - +
120D LEU* 1.3 59.9 + - - +
127D PHE* 3.4 21.4 - - + -
129D ILE* 5.3 7.4 - - + -
382D LEU* 6.0 0.9 - - + -
386D PHE* 3.7 40.2 - - + -
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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