Contacts of the strand formed by residues 129 - 141 (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 TRP 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PHE* 3.6 13.7 - - + -
82A SER* 3.5 32.3 - - - -
83A GLY* 3.1 46.5 + - - +
84A LYS* 3.4 10.7 - - - +
95A LEU* 3.7 23.3 - - + +
97A LEU* 3.8 13.2 - - + -
121A VAL* 4.0 21.0 - - + +
125A LEU* 4.2 22.7 - - + -
127A GLU 4.6 0.7 - - - -
128A PRO* 1.3 75.8 - - - +
130A LEU* 1.3 71.0 + - - +
131A HIS* 4.1 22.4 - + + +
156A HIS* 3.4 34.1 - + + -
119B LYS* 4.9 4.3 - - - +
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Residues in contact with LEU 130 (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 VAL* 3.6 21.8 - - + -
81A PHE 3.2 19.5 - - - +
82A SER* 3.6 16.8 - - - -
129A TRP* 1.3 78.9 - - - +
131A HIS* 1.3 64.0 + - - +
132A SER* 6.0 2.0 - - - -
158A VAL* 4.5 3.1 - - + -
118B GLN* 3.1 56.8 - - + +
119B LYS* 2.9 38.2 + - + +
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Residues in contact with HIS 131 (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 VAL* 3.5 3.0 - - - +
81A PHE* 2.7 43.2 + - + +
97A LEU* 4.1 26.0 - - + -
119A LYS* 3.6 45.0 + - + +
121A VAL* 4.4 18.0 - - + +
125A LEU* 6.3 0.2 - - - +
129A TRP* 4.1 16.5 - + + +
130A LEU* 1.3 86.4 + - - +
132A SER* 1.3 60.4 + - - +
133A MET* 5.4 3.1 - - + -
119B LYS* 4.1 16.8 + - - -
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Residues in contact with SER 132 (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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78A GLN* 4.6 7.8 - - - +
79A VAL 3.6 10.0 + - - -
80A VAL* 3.7 18.0 - - - +
130A LEU* 4.4 2.2 + - - -
131A HIS* 1.3 76.1 - - - +
133A MET* 1.3 69.2 + - - +
134A TYR* 4.3 1.3 + - - +
117B SER* 4.2 16.1 + - - -
118B GLN 6.0 2.2 - - - -
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Residues in contact with MET 133 (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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77A SER 3.9 1.0 - - - +
78A GLN* 3.3 6.6 - - - -
79A VAL* 2.9 40.2 + - + +
81A PHE* 3.8 23.3 - - - -
97A LEU* 4.9 1.8 - - - -
98A ALA* 3.7 4.7 - - - -
99A HIS* 3.2 33.3 - - + +
117A SER* 3.2 53.4 - - - +
118A GLN 4.5 13.0 - - - +
119A LYS* 4.7 6.5 - - + -
131A HIS* 5.9 1.3 - - + -
132A SER* 1.3 81.2 + - - +
134A TYR* 1.3 59.0 + - - +
135A HIS* 4.9 4.8 - - + -
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Residues in contact with TYR 134 (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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74A PHE* 4.7 1.3 - + - -
76A TYR* 3.7 21.2 - + + +
77A SER 3.6 11.9 - - - -
78A GLN* 3.4 23.8 - - + +
117A SER* 4.7 1.6 + - - -
132A SER* 4.3 1.4 + - - +
133A MET* 1.3 72.0 - - - +
135A HIS* 1.3 93.9 + - - +
136A GLY* 4.1 1.3 - - - -
165A PHE* 3.9 13.2 - + - -
74B PHE* 3.7 11.5 - + - -
134B TYR* 3.7 31.2 - + + +
135B HIS* 4.0 2.2 - - + -
136B GLY* 2.6 42.5 + - - -
78D GLN* 4.1 1.6 - - - +
132D SER* 5.8 0.3 + - - -
134D TYR* 3.7 46.8 - + + +
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Residues in contact with HIS 135 (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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76A TYR* 3.3 1.9 - - - +
77A SER 3.0 33.7 + - - +
99A HIS* 3.8 31.8 + + - -
101A VAL* 4.5 7.9 - - + +
115A LEU* 3.3 42.8 + - + +
116A SER 3.9 4.1 + - - -
117A SER* 3.0 39.7 + - - -
133A MET* 4.9 5.2 - - + -
134A TYR* 1.3 95.7 + - - +
136A GLY* 1.3 58.8 + - - +
78D GLN* 3.5 18.4 + - - +
134D TYR* 4.1 6.7 - - + -
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Residues in contact with GLY 136 (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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74A PHE* 3.7 14.7 - - - -
75A VAL 3.1 13.0 - - - -
76A TYR* 3.9 4.3 - - - -
115A LEU* 3.8 4.7 - - - -
134A TYR* 4.1 0.9 - - - -
135A HIS* 1.3 76.5 - - - +
137A ALA* 1.3 63.4 + - - +
76D TYR* 3.8 6.1 - - - -
134D TYR* 2.6 37.2 + - - -
165D PHE* 4.0 0.5 - - - -
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Residues in contact with ALA 137 (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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74A PHE* 3.4 9.9 - - - -
75A VAL 2.9 29.8 + - - -
115A LEU* 3.8 8.4 - - + +
136A GLY* 1.3 75.5 - - - +
138A ALA* 1.3 61.7 + - - +
139A PHE* 3.3 24.0 - - + -
32D HIS* 3.5 19.7 - - + -
76D TYR* 3.5 22.9 - - + -
165D PHE* 4.2 2.0 - - + -
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Residues in contact with ALA 138 (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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72A ILE* 4.1 16.2 - - + -
73A TYR 3.2 8.5 - - - +
74A PHE* 4.1 1.1 - - - +
137A ALA* 1.3 72.7 - - - +
139A PHE* 1.3 68.5 + - - +
171A LEU* 4.5 2.7 - - + -
30D ALA* 5.2 1.8 - - + -
31D ALA 5.0 3.6 - - - +
32D HIS* 3.6 21.8 - - - +
53D PHE* 3.6 10.3 - - + -
76D TYR* 2.8 19.9 + - + +
169D PHE* 4.3 23.3 - - + -
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Residues in contact with PHE 139 (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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72A ILE* 3.4 3.3 - - - -
73A TYR* 2.7 35.6 + - - +
75A VAL* 3.9 22.0 - - + -
114A LEU* 3.6 57.9 - - + -
115A LEU* 3.7 18.8 - - + -
137A ALA* 3.3 37.9 - - + -
138A ALA* 1.3 76.5 - - - +
140A GLN* 1.3 61.5 + - - +
141A LEU* 3.5 24.4 + - + +
32D HIS* 4.0 21.8 - + - -
51D ARG* 4.6 15.7 - - + +
53D PHE* 4.2 5.2 - - - -
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Residues in contact with GLN 140 (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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71A GLY 3.7 5.4 - - - +
72A ILE* 3.1 21.5 - - + -
139A PHE* 1.3 70.9 - - - +
141A LEU* 1.3 66.4 + - - +
142A THR* 5.3 1.6 - - - +
51D ARG* 4.0 15.9 + - - +
52D ALA 5.0 0.7 - - - +
53D PHE* 3.3 48.8 - - + +
54D LEU 4.6 2.2 + - - -
55D GLN* 4.0 18.3 - - - +
30X SER* 5.6 0.8 + - - -
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Residues in contact with LEU 141 (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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67A VAL* 3.7 31.4 - - + -
70A SER* 3.5 2.0 - - - -
71A GLY 3.0 30.0 + - - +
73A TYR* 3.8 25.8 - - + -
75A VAL* 4.4 5.8 - - + -
103A LEU* 3.9 30.5 - - + -
114A LEU* 4.9 3.1 - - + -
139A PHE* 3.9 20.4 - - + +
140A GLN* 1.3 81.5 - - - +
142A THR* 1.3 68.0 + - - +
145A ASP* 3.4 7.4 - - - +
147A LEU* 3.9 23.8 - - + -
51D ARG* 4.9 2.2 - - - +
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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