Contacts of the helix formed by residues 87 - 105 (chain A) in PDB entry 2PMW
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 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLU 3.2 5.2 + - - +
86A THR* 1.3 73.7 - - - +
88A LEU* 1.3 76.3 + - + +
89A SER* 2.8 43.5 + - - -
90A GLN* 2.8 35.0 + - + +
91A SER* 2.9 14.0 + - - -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR 4.1 0.8 + - - -
87A HIS* 1.3 85.3 + - + +
89A SER* 1.3 61.8 + - - +
91A SER* 3.2 5.9 + - - -
92A GLU* 3.0 50.4 + - - +
114A VAL* 3.9 17.5 - - + -
115A PHE 4.2 3.6 - - - +
116A HIS* 3.5 55.4 - - + +
120A PRO* 6.0 0.2 - - - +
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 2.8 28.6 + - - -
88A LEU* 1.3 73.3 - - - +
90A GLN* 1.3 63.9 + - - +
92A GLU* 3.4 13.4 + - - +
93A ARG* 3.2 54.7 + - - +
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU* 4.5 5.5 - - - +
86A THR* 3.6 15.8 - - + -
87A HIS* 2.8 40.4 + - + +
89A SER* 1.3 74.1 - - - +
91A SER* 1.3 66.8 + - - +
93A ARG* 3.2 9.3 + - - +
94A THR* 2.9 28.2 + - - -
139A HIS* 3.6 27.5 - - - +
302A SO4 3.4 35.7 + - - +
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Residues in contact with SER 91 (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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82A LEU* 3.4 27.8 - - - +
86A THR* 3.8 4.9 - - - +
87A HIS 2.9 13.4 + - - -
88A LEU* 3.4 12.9 - - - -
90A GLN* 1.3 78.6 - - - +
92A GLU* 1.3 61.6 + - - +
94A THR* 3.3 2.6 + - - -
95A ALA* 3.1 22.5 + - - +
114A VAL* 4.2 17.7 - - - -
115A PHE 4.7 1.7 + - - -
120A PRO* 4.0 5.9 - - - +
121A GLY* 3.7 15.7 + - - -
122A PHE* 3.9 5.6 - - - -
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Residues in contact with GLU 92 (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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88A LEU* 3.0 48.3 + - + +
89A SER* 3.7 11.4 + - - +
90A GLN 3.1 0.2 - - - -
91A SER* 1.3 76.1 - - - +
93A ARG* 1.3 60.8 + - + +
95A ALA* 3.4 7.6 + - - +
96A ARG* 3.1 37.9 + - + +
114A VAL* 4.2 18.1 - - + +
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Residues in contact with ARG 93 (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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89A SER* 3.2 44.0 + - - +
90A GLN* 3.2 10.6 + - - +
92A GLU* 1.3 75.6 - - + +
94A THR* 1.3 60.1 + - - +
96A ARG* 3.3 13.7 + - - +
97A ARG* 2.8 30.9 + - - +
302A SO4 3.0 35.3 + - - +
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Residues in contact with THR 94 (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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82A LEU* 4.4 11.8 - - + +
90A GLN 2.9 18.3 + - - -
91A SER* 3.6 6.7 - - - -
93A ARG* 1.3 77.2 - - - +
95A ALA* 1.3 57.1 + - - +
97A ARG* 3.3 7.5 + - - +
98A LEU* 3.0 26.9 + - - +
122A PHE* 4.0 13.7 - - + -
137A LEU* 3.8 27.6 - - + +
138A PRO* 3.6 31.7 + - + +
139A HIS* 3.8 11.6 - - - -
140A VAL* 4.8 0.4 - - + -
302A SO4 5.1 0.3 + - - -
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Residues in contact with ALA 95 (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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91A SER 3.1 14.2 + - - +
92A GLU* 3.7 10.5 - - - +
93A ARG 3.2 0.2 - - - -
94A THR* 1.3 75.7 - - - +
96A ARG* 1.3 63.2 + - + +
98A LEU* 3.2 4.0 + - - +
99A GLN* 3.1 28.0 + - - +
111A ILE* 4.0 23.7 - - + +
114A VAL* 5.3 3.4 - - + -
122A PHE* 3.8 32.5 - - + -
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Residues in contact with ARG 96 (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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92A GLU* 3.1 26.5 + - - +
93A ARG* 3.7 12.0 - - - +
95A ALA* 1.3 76.3 - - + +
97A ARG* 1.3 62.8 + - - +
99A GLN* 3.4 12.7 + - - +
100A ALA* 3.0 25.0 + - - +
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Residues in contact with ARG 97 (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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93A ARG 2.8 19.4 + - - +
94A THR* 3.6 7.6 - - - +
95A ALA 3.2 0.2 - - - -
96A ARG* 1.3 78.1 - - - +
98A LEU* 1.3 57.1 + - - +
100A ALA* 3.7 5.0 - - - +
101A GLN* 2.9 58.5 + - + +
104A ARG* 5.8 1.7 - - - +
137A LEU* 3.8 18.2 - - + -
138A PRO* 3.8 30.0 - - - +
301A SO4 4.9 4.6 + - - -
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Residues in contact with LEU 98 (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* 5.0 1.8 - - + -
94A THR 3.0 8.4 + - - +
95A ALA* 3.2 9.4 + - - +
97A ARG* 1.3 75.2 - - - +
99A GLN* 1.3 57.2 + - + +
101A GLN* 3.4 1.7 + - - -
102A ALA* 2.7 43.8 + - + +
109A THR* 5.3 1.6 - - + -
111A ILE* 5.1 0.7 - - + -
122A PHE* 3.9 25.8 - - + -
124A VAL* 4.2 12.6 - - + -
126A MET* 3.9 29.8 - - + -
130A LEU* 4.9 3.4 - - + +
133A LEU* 4.5 15.9 - - + -
134A ALA* 4.1 19.5 - - + +
137A LEU* 3.6 28.5 - - + +
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Residues in contact with GLN 99 (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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95A ALA 3.1 13.4 + - - +
96A ARG* 3.7 14.3 - - - +
98A LEU* 1.3 78.7 - - + +
100A ALA* 1.3 54.0 + - - +
102A ALA* 3.5 2.2 - - - +
103A ALA* 2.8 34.5 + - - +
107A TYR 4.8 0.5 - - - +
109A THR* 3.1 48.1 + - - +
110A LYS* 4.1 2.8 - - - +
111A ILE* 3.6 30.6 - - + +
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Residues in contact with ALA 100 (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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96A ARG 3.0 17.3 + - - +
97A ARG* 3.7 7.0 - - - +
99A GLN* 1.3 74.4 - - - +
101A GLN* 1.3 65.6 + - - +
103A ALA* 3.0 8.9 + - - +
104A ARG* 3.0 48.0 + - - +
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Residues in contact with GLN 101 (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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97A ARG* 2.9 49.7 + - + +
98A LEU* 3.9 3.0 - - - +
100A ALA* 1.3 76.1 - - - +
102A ALA* 1.3 62.6 + - - +
103A ALA 3.4 0.3 + - - -
104A ARG* 3.4 11.7 + - - +
105A ARG* 2.7 37.1 + - - +
133A LEU* 3.5 34.8 + - + +
137A LEU* 3.5 24.4 - - - +
301A SO4 3.3 32.3 + - - +
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Residues in contact with ALA 102 (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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98A LEU* 2.7 25.9 + - + +
99A GLN 3.5 3.4 - - - +
101A GLN* 1.3 73.6 - - - +
103A ALA* 1.3 60.6 + - - +
105A ARG* 3.1 8.7 + - - +
106A GLY 3.3 0.3 + - - -
107A TYR* 2.9 28.6 + - - +
109A THR* 3.5 31.9 - - + -
130A LEU* 3.9 25.4 - - + -
133A LEU* 4.3 0.8 - - - +
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Residues in contact with ALA 103 (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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99A GLN 2.8 18.1 + - - +
100A ALA* 3.0 8.0 + - - +
102A ALA* 1.3 73.4 - - - +
104A ARG* 1.3 61.9 + - + +
105A ARG 2.9 6.6 + - - -
106A GLY* 3.0 12.6 + - - -
107A TYR 3.7 11.0 + - - +
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Residues in contact with ARG 104 (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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97A ARG* 5.8 1.8 - - - +
100A ALA* 3.0 33.9 + - - +
101A GLN* 3.7 22.4 - - - +
102A ALA 3.3 0.4 - - - -
103A ALA* 1.3 75.8 - - + +
105A ARG* 1.3 61.9 + - - +
106A GLY 3.4 0.4 + - - -
301A SO4 2.8 49.8 + - - +
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Residues in contact with ARG 105 (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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101A GLN* 2.7 37.3 + - - +
102A ALA 3.1 8.4 + - - +
103A ALA 2.9 0.6 - - - -
104A ARG* 1.3 81.7 - - + +
106A GLY* 1.3 59.2 + - - +
107A TYR* 3.4 26.9 - - + -
130A LEU* 4.9 5.4 - - - -
133A LEU* 4.0 35.6 - - - +
301A SO4 2.7 41.2 + - - -
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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