Contacts of the strand formed by residues 129 - 141 (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 TRP 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D PHE* 3.7 2.9 - - + -
82D SER* 3.3 31.2 - - - -
83D GLY* 3.1 52.0 + - - +
84D LYS 3.8 2.7 - - - +
85D ALA* 4.2 11.9 - - + +
95D LEU* 3.7 21.3 - - + -
97D LEU* 3.6 32.8 - - + -
121D VAL* 3.7 18.1 - - + +
125D LEU* 3.8 31.4 - - + -
128D PRO* 1.3 76.1 - - + +
130D LEU* 1.3 81.3 + - - +
131D HIS* 4.1 24.0 - + + +
156D HIS* 3.8 15.7 - + + -
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Residues in contact with LEU 130 (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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118A GLN* 3.4 55.2 - - + +
119A LYS* 3.3 30.5 - - + +
120A MET* 5.4 6.7 - - + +
80D VAL* 3.8 18.6 - - + -
81D PHE 3.3 11.7 - - - +
82D SER* 3.6 22.2 - - - -
129D TRP* 1.3 81.0 - - - +
131D HIS* 1.3 73.4 + - - +
132D SER* 4.3 2.1 + - - -
158D VAL* 4.7 3.6 - - + -
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Residues in contact with HIS 131 (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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119A LYS* 4.4 14.9 + - - +
80D VAL* 3.4 2.5 - - - -
81D PHE* 2.7 44.9 + - + +
97D LEU* 4.5 17.0 - - + -
119D LYS* 3.6 45.2 + - + +
121D VAL* 4.4 15.9 - - + +
125D LEU* 6.2 0.8 - - + +
129D TRP* 4.1 22.7 - + + +
130D LEU* 1.3 100.0 + - - +
132D SER* 1.3 60.6 + - - +
133D MET* 5.1 3.6 - - + -
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Residues in contact with SER 132 (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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117A SER* 4.3 18.8 + - - -
118A GLN 5.4 7.2 - - - -
134A TYR 5.8 0.3 + - - -
78D GLN* 4.5 6.6 + - - -
79D VAL 3.6 7.5 + - - -
80D VAL* 3.8 20.4 - - - +
130D LEU* 4.2 2.4 - - - -
131D HIS* 1.3 74.4 - - - +
133D MET* 1.3 67.4 + - - +
134D TYR* 4.3 1.8 + - - +
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Residues in contact with MET 133 (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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77D SER 4.0 0.6 - - - +
78D GLN* 3.2 5.9 - - - +
79D VAL* 2.9 39.6 + - + +
81D PHE* 3.9 23.1 - - + -
97D LEU* 5.1 1.1 - - - +
98D ALA* 4.6 2.5 - - - -
99D HIS* 3.5 33.8 - - + +
117D SER* 3.3 49.8 - - - +
118D GLN 4.6 12.6 - - - +
119D LYS* 4.9 7.4 - - + -
131D HIS* 5.1 4.5 - - + -
132D SER* 1.3 82.6 + - - +
134D TYR* 1.3 60.3 + - - +
135D HIS* 4.7 4.9 - - - +
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Residues in contact with TYR 134 (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* 4.0 8.5 - - - -
134A TYR* 3.7 36.9 - + + +
135A HIS* 4.1 2.7 - - - -
136A GLY* 2.6 44.5 + - - -
78B GLN* 4.1 1.0 - - - +
134B TYR* 3.6 40.4 - + + +
74D PHE* 4.7 2.4 - - - -
76D TYR* 3.7 19.0 - - + +
77D SER 3.5 8.5 - - - -
78D GLN* 3.6 30.1 - - + +
132D SER* 4.3 2.0 - - - +
133D MET* 1.3 74.8 - - - +
135D HIS* 1.3 81.9 + - - +
136D GLY 4.4 0.2 - - - -
165D PHE* 3.9 12.6 - + - -
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Residues in contact with HIS 135 (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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78B GLN* 3.1 22.0 - - - +
134B TYR* 4.0 7.0 - - + -
165B PHE* 4.7 2.7 - - + -
76D TYR* 3.3 2.4 - - - +
77D SER 2.9 39.6 + - - +
99D HIS* 3.9 21.5 + + - -
101D VAL* 4.8 6.5 - - + -
115D LEU* 3.4 39.0 - - + +
116D SER 3.6 15.3 - - - -
117D SER* 3.1 34.5 + - - -
133D MET* 4.7 5.0 - - - +
134D TYR* 1.3 95.6 - - - +
136D GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 136 (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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76B TYR* 3.8 4.5 - - - -
134B TYR* 2.7 37.4 + - - -
165B PHE* 3.9 0.9 - - - -
74D PHE* 3.7 9.2 - - - -
75D VAL 3.0 14.6 - - - -
76D TYR* 3.9 4.5 - - - -
115D LEU* 3.7 5.3 - - - +
134D TYR* 5.0 0.7 - - - -
135D HIS* 1.3 78.1 - - - +
137D ALA* 1.3 65.5 + - - +
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B HIS* 3.6 18.6 - - + -
76B TYR* 3.5 18.2 - - + -
165B PHE* 4.2 2.2 - - + -
74D PHE* 3.5 16.6 - - - -
75D VAL 2.9 28.3 + - - -
115D LEU* 3.9 7.5 - - + +
136D GLY* 1.3 76.9 - - - +
138D ALA* 1.3 61.4 - - - +
139D PHE* 3.2 23.4 - - + -
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Residues in contact with ALA 138 (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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30B ALA* 5.3 0.9 - - + -
31B ALA 5.3 2.2 - - - +
32B HIS* 3.7 12.2 + - + -
53B PHE* 3.6 30.4 - - + -
76B TYR* 3.0 17.5 + - - +
168B ALA 5.8 0.2 - - - +
169B PHE* 4.4 14.6 - - + -
72D ILE* 4.2 9.4 - - + -
73D TYR 3.1 9.0 - - - +
74D PHE* 4.0 1.7 - - + +
137D ALA* 1.3 72.0 - - - +
139D PHE* 1.3 68.7 + - - +
171D LEU* 4.4 11.7 - - + -
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Residues in contact with PHE 139 (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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32B HIS* 4.6 11.9 - + - -
51B ARG* 4.7 21.8 - - + +
53B PHE* 4.4 2.2 - - - -
161B PRO 6.0 0.4 - - - -
165B PHE* 6.0 0.2 - + - -
72D ILE* 4.3 4.0 - - - -
73D TYR 2.7 35.0 + - - +
75D VAL* 3.9 16.4 - - + -
114D LEU* 3.5 44.2 - - + -
115D LEU* 3.5 36.8 - - + -
137D ALA* 3.2 39.9 - - + -
138D ALA* 1.3 77.9 - - - +
140D GLN* 1.3 62.4 + - - +
141D LEU* 3.5 24.1 + - + +
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Residues in contact with GLN 140 (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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49B THR 5.7 0.4 + - - -
51B ARG* 3.7 22.8 + - - +
52B ALA 4.2 5.3 + - - +
53B PHE* 3.1 47.4 - - + +
55B GLN* 4.6 4.5 - - - +
71D GLY 3.6 7.4 - - - +
72D ILE* 3.8 18.7 - - + +
103D LEU* 5.5 0.2 - - - +
139D PHE* 1.3 70.8 - - - +
141D LEU* 1.3 68.2 + - - +
142D THR* 5.7 0.6 - - - +
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Residues in contact with LEU 141 (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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51B ARG* 5.1 0.9 - - - +
67D VAL* 3.9 17.7 - - + -
70D SER* 3.3 1.4 - - - -
71D GLY 2.8 31.1 + - - +
73D TYR* 4.0 30.7 - - + -
75D VAL* 4.3 7.2 - - + -
103D LEU* 4.0 22.2 - - + -
114D LEU* 4.9 1.8 - - + -
139D PHE* 3.8 18.2 - - + +
140D GLN* 1.3 85.0 - - - +
142D THR* 1.3 65.7 + - - +
145D ASP* 3.3 12.6 - - - +
147D LEU* 3.9 37.9 - - + -
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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