Contacts of the strand formed by residues 111 - 121 (chain B) 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 HIS 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B GLN* 3.8 36.2 + - + +
103B LEU 3.7 5.2 - - - +
104B PHE* 4.1 22.3 - + + +
105B SER* 4.9 0.8 - - - -
109B PRO* 3.0 15.0 + - - +
110B PHE* 1.3 104.4 + + + +
112B VAL* 1.3 60.9 + - - +
113B PRO* 3.8 7.5 - - - +
148B SER* 5.1 5.2 - - - -
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ARG* 4.6 27.4 - - + +
100B GLU* 4.9 0.2 - - - -
102B GLN* 3.6 2.9 - - - -
103B LEU* 3.0 52.9 + - + +
105B SER* 4.9 12.0 - - - -
111B HIS* 1.3 72.6 - - - +
113B PRO* 1.3 82.4 - - + +
114B LEU* 3.7 1.9 + - + +
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Residues in contact with PRO 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ARG* 5.6 2.1 - - - +
161A PRO* 5.9 2.1 - - - +
162A SER* 3.9 12.1 + - - +
100B GLU* 3.3 29.2 - - + +
101B VAL 3.9 5.2 - - - +
102B GLN* 4.7 0.2 - - - -
111B HIS 3.8 7.0 - - - +
112B VAL* 1.3 98.2 - - + +
114B LEU* 1.3 63.5 + - - +
116B SER* 4.0 19.3 - - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.9 32.5 - - - +
161A PRO 4.5 2.4 - - - +
162A SER* 3.3 18.2 - - - -
165A PHE* 5.1 0.5 - - - -
75B VAL* 5.5 0.7 - - + -
101B VAL* 2.9 19.2 + - + +
102B GLN 4.5 1.8 - - - -
103B LEU* 4.1 23.3 - - + +
112B VAL* 4.3 4.3 - - + +
113B PRO* 1.3 79.5 - - - +
115B LEU* 1.3 74.1 + - + +
139B PHE* 3.4 52.8 - - + -
141B LEU* 5.0 0.7 - - + -
147B LEU* 3.9 28.5 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A SER 3.9 2.5 - - - -
165A PHE* 4.0 20.6 - - + -
75B VAL 3.6 27.1 - - - +
76B TYR* 4.6 0.4 - - - -
99B HIS 4.1 0.2 - - - +
100B GLU* 3.1 8.8 - - - +
101B VAL* 2.9 45.6 + - + -
114B LEU* 1.3 90.6 - - + +
116B SER* 1.3 63.0 + - - +
135B HIS* 3.7 28.5 - - + +
136B GLY* 3.7 11.9 - - - +
137B ALA* 3.9 16.2 - - + +
139B PHE* 3.6 21.5 - - + -
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Residues in contact with SER 116 (chain B).
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* 4.1 5.9 + - - -
80A VAL* 5.1 2.9 - - - +
162A SER* 2.8 39.0 + - - +
163A THR* 4.1 18.2 - - - +
99B HIS 4.0 2.7 - - - -
100B GLU* 4.6 7.1 - - - +
113B PRO* 4.0 10.2 - - - +
115B LEU* 1.3 74.7 + - - +
117B SER* 1.3 68.3 + - - +
118B GLN* 6.3 1.1 - - - -
135B HIS* 3.5 8.3 + - - -
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Residues in contact with SER 117 (chain B).
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* 5.2 0.3 + - - -
80A VAL* 5.8 0.8 - - - +
132A SER* 4.2 16.6 + - - -
98B ALA* 3.3 3.1 - - - +
99B HIS 3.1 32.7 + - - -
116B SER* 1.3 74.0 + - - +
118B GLN* 1.3 67.6 + - - +
133B MET* 3.3 33.2 - - - +
134B TYR 5.4 0.5 + - - -
135B HIS* 2.9 27.5 + - - -
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.1 38.0 - - + +
132A SER* 6.0 1.9 - - - -
96B TYR* 2.9 38.1 + - + +
97B LEU 3.5 10.1 - - - +
98B ALA* 4.3 1.3 - - + +
116B SER* 6.3 1.6 - - - -
117B SER* 1.3 79.8 - - - +
119B LYS* 1.3 66.6 + - - +
133B MET* 4.6 5.7 - - - +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP* 4.7 3.8 - - - +
130A LEU* 2.9 45.6 + - + +
131A HIS* 4.1 16.7 + - - -
96B TYR* 4.0 4.2 - - - -
97B LEU* 3.0 46.8 + - + +
118B GLN* 1.3 79.4 - - - +
120B MET* 1.3 76.8 + - - +
121B VAL 4.1 0.2 - - - -
131B HIS* 4.2 36.1 - - + +
133B MET* 4.8 7.6 - - + -
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 5.8 3.1 - - - +
94B PRO* 4.4 17.5 - - + +
95B LEU 3.5 14.4 - - - +
96B TYR* 4.2 28.3 - - + -
119B LYS* 1.3 90.9 + - - +
121B VAL* 1.3 60.3 + - - +
122B TYR* 3.5 46.2 - - + +
131B HIS* 5.5 0.4 - - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LYS* 4.4 8.5 + - - -
94B PRO* 3.9 0.7 - - - +
95B LEU* 2.9 64.2 + - + +
97B LEU* 4.0 14.4 - - + -
119B LYS 4.1 0.2 - - - -
120B MET* 1.3 72.1 - - - +
122B TYR* 1.3 72.6 + - - +
125B LEU* 3.9 14.1 - - + -
129B TRP* 3.7 32.8 - - + +
131B HIS* 4.2 17.3 + - - +
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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