Contacts of the helix formed by residues 120 - 125 (chain I) in PDB entry 3MQT
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 PRO 120 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118I GLY 4.6 1.1 - - - +
119I VAL* 1.3 88.6 - - + +
121I ALA* 1.3 60.7 + - - +
122I TYR* 3.3 44.0 - - + +
123I LYS* 2.9 42.5 + - + +
124I LEU 3.8 1.7 + - - -
322I HIS* 3.9 1.6 - - + -
364I SER 3.9 2.7 - - - +
365I ASP* 3.7 28.9 - - + +
366I LYS 3.4 19.3 - - - +
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Residues in contact with ALA 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I TYR* 4.1 15.2 - - + +
119I VAL 3.6 2.3 + - - -
120I PRO* 1.3 70.3 - - - +
122I TYR* 1.3 58.1 + - - +
124I LEU* 2.8 30.7 + - - +
125I MET* 3.0 31.3 + - + +
322I HIS* 3.6 8.0 - - - +
368I GLY* 2.9 30.7 + - - +
369I LEU* 4.0 9.9 - - + -
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Residues in contact with TYR 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I PRO* 3.1 30.9 + - + +
121I ALA* 1.3 75.8 - - - +
123I LYS* 1.3 73.9 + - + +
125I MET* 3.2 16.0 + - - -
126I GLY 3.5 0.3 + - - -
127I GLY* 2.9 23.2 + - - -
128I ALA* 3.8 28.3 - - + -
322I HIS* 2.9 36.2 + + - +
325I ILE* 3.6 21.1 - - + -
326I VAL* 3.5 6.7 - - + +
363I VAL* 4.0 16.3 + - + -
364I SER 3.9 12.3 - - - -
365I ASP* 4.1 10.2 - - - +
77K GLU* 3.8 18.2 - - - -
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Residues in contact with LYS 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I VAL* 4.0 14.8 - - + -
120I PRO* 2.9 32.4 + - + +
122I TYR* 1.3 100.3 + - + +
124I LEU* 1.3 60.9 + - - +
125I MET 3.1 0.9 + - - -
126I GLY* 3.4 8.5 + - - -
127I GLY* 3.8 8.8 + - - +
74K ASP* 2.6 34.6 + - - +
76K LEU* 3.9 34.1 - - + +
77K GLU* 2.9 30.7 + - + +
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Residues in contact with LEU 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I LEU* 4.4 14.4 - - + -
78I PHE* 4.0 23.1 - - + -
110I TYR* 4.1 19.7 - - + +
113I ALA* 3.7 17.0 - - + +
114I GLY* 3.4 37.2 - - - +
117I LEU* 4.0 22.0 - - + -
119I VAL* 3.9 13.7 - - + -
121I ALA* 2.8 17.0 + - - +
123I LYS* 1.3 72.1 - - - +
125I MET* 1.3 58.2 + - - +
126I GLY 3.3 2.3 + - - -
293I LEU* 5.4 0.9 - - - +
76K LEU* 4.1 16.6 - - + -
124K LEU* 6.0 0.2 - - + -
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Residues in contact with MET 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I TYR* 4.1 12.6 - - + -
121I ALA* 3.0 24.9 + - + +
122I TYR* 3.6 9.4 - - - +
123I LYS 3.1 1.0 - - - -
124I LEU* 1.3 79.2 - - - +
126I GLY* 1.3 56.7 + - - +
127I GLY 3.6 1.3 - - - -
289I VAL* 3.9 40.8 - - + -
293I LEU* 3.9 23.0 - - + +
296I MET* 5.7 0.3 - - - +
319I ALA 4.8 1.3 - - - +
322I HIS* 3.6 26.2 - - + +
323I PHE* 3.7 31.0 - - - +
326I VAL* 3.5 24.5 - - + +
369I LEU* 4.4 8.5 - - + -
79K ARG* 5.1 2.9 - - - +
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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